ReadVtk.cpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation. Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */
 
/**
 * \class ReadVtk
 * \brief VTK reader from Mesquite
 * \author Jason Kraftcheck
 */
 
#include <cassert>
#include <cstdlib>
#include <cstring>
 
#include "ReadVtk.hpp"
#include "moab/Range.hpp"
#include "Internals.hpp"
#include "moab/Interface.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/FileOptions.hpp"
#include "FileTokenizer.hpp"
#include "moab/VtkUtil.hpp"
#include "MBTagConventions.hpp"
 
// #define MB_VTK_MATERIAL_SETS
#ifdef MB_VTK_MATERIAL_SETS
#include <map>
#endif
 
namespace moab
{
 
#ifdef MB_VTK_MATERIAL_SETS
 
class Hash
{
 public:
 unsigned long value;
 
 Hash()
 {
 this->value = 5381L;
 }
 
 Hash( const unsigned char* bytes, size_t len )
 { // djb2, a hash by dan bernstein presented on comp.lang.c for hashing strings.
 this->value = 5381L;
 for( ; len; --len, ++bytes )
 this->value = this->value * 33 + ( *bytes );
 }
 
 Hash( bool duh )
 {
 this->value = duh; // Hashing a single bit with a long is stupid but easy.
 }
 
 Hash( const Hash& src )
 {
 this->value = src.value;
 }
 
 Hash& operator=( const Hash& src )
 {
 this->value = src.value;
 return *this;
 }
 
 bool operator<( const Hash& other ) const
 {
 return this->value < other.value;
 }
};
 
// Pass this class opaque data + a handle and it adds the handle to a set
// whose opaque data has the same hash. If no set exists for the hash,
// it creates one. Each set is tagged with the opaque data.
// When entities with different opaque data have the same hash, they
// will be placed into the same set.
// There will be no collisions when the opaque data is shorter than an
// unsigned long, and this is really the only case we need to support.
// The rest is bonus. Hash does quite well with strings, even those
// with identical prefixes.
class Modulator : public std::map< Hash, EntityHandle >
{
 public:
 Modulator( Interface* iface ) : mesh( iface ) {}
 
 ErrorCode initialize( std::string tag_name, DataType mb_type, size_t sz, size_t per_elem )
 {
 std::vector< unsigned char > default_val;
 default_val.resize( sz * per_elem );
 ErrorCode rval = this->mesh->tag_get_handle( tag_name.c_str(), per_elem, mb_type, this->tag,
 MB_TAG_SPARSE | MB_TAG_BYTES | MB_TAG_CREAT, &default_val[0] );
 return rval;
 }
 
 void add_entity( EntityHandle ent, const unsigned char* bytes, size_t len )
 {
 Hash h( bytes, len );
 EntityHandle mset = this->congruence_class( h, bytes );
 ErrorCode rval;
 rval = this->mesh->add_entities( mset, &ent, 1 );MB_CHK_SET_ERR_RET( rval, "Failed to add entities to mesh" );
 }
 
 void add_entities( Range& range, const unsigned char* bytes, size_t bytes_per_ent )
 {
 for( Range::iterator it = range.begin(); it != range.end(); ++it, bytes += bytes_per_ent )
 {
 Hash h( bytes, bytes_per_ent );
 EntityHandle mset = this->congruence_class( h, bytes );
 ErrorCode rval;
 rval = this->mesh->add_entities( mset, &*it, 1 );MB_CHK_SET_ERR_RET( rval, "Failed to add entities to mesh" );
 }
 }
 
 EntityHandle congruence_class( const Hash& h, const void* tag_data )
 {
 std::map< Hash, EntityHandle >::iterator it = this->find( h );
 if( it == this->end() )
 {
 EntityHandle mset;
 Range preexist;
 ErrorCode rval;
 rval = this->mesh->get_entities_by_type_and_tag( 0, MBENTITYSET, &this->tag, &tag_data, 1, preexist );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to get entities by type and tag", (EntityHandle)0 );
 if( preexist.size() )
 {
 mset = *preexist.begin();
 }
 else
 {
 rval = this->mesh->create_meshset( MESHSET_SET, mset );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to create mesh set", (EntityHandle)0 );
 rval = this->mesh->tag_set_data( this->tag, &mset, 1, tag_data );MB_CHK_SET_ERR_RET_VAL( rval, "Failed to set tag data", (EntityHandle)0 );
 }
 ( *this )[h] = mset;
 return mset;
 }
 return it->second;
 }
 
 Interface* mesh;
 Tag tag;
};
#endif // MB_VTK_MATERIAL_SETS
 
ReaderIface* ReadVtk::factory( Interface* iface )
{
 return new ReadVtk( iface );
}
 
ReadVtk::ReadVtk( Interface* impl ) : mdbImpl( impl ), mPartitionTagName( MATERIAL_SET_TAG_NAME )
{
 mdbImpl->query_interface( readMeshIface );
}
 
ReadVtk::~ReadVtk()
{
 if( readMeshIface )
 {
 mdbImpl->release_interface( readMeshIface );
 readMeshIface = 0;
 }
}
 
const char* const vtk_type_names[] = {
 "bit", "char", "unsigned_char", "short", "unsigned_short", "int", "unsigned_int",
 "long", "unsigned_long", "float", "double", "vtkIdType", 0 };
 
ErrorCode ReadVtk::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 ReadVtk::load_file( const char* filename,
 const EntityHandle* /* file_set */,
 const FileOptions& opts,
 const ReaderIface::SubsetList* subset_list,
 const Tag* file_id_tag )
{
 ErrorCode result;
 
 int major, minor;
 char vendor_string[257];
 std::vector< Range > element_list;
 Range vertices;
 
 if( subset_list )
 {
 MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Reading subset of files not supported for VTK" );
 }
 
 // Does the caller want a field to be used for partitioning the entities?
 // If not, we'll assume any scalar integer field named MATERIAL_SET specifies partitions.
 std::string partition_tag_name;
 result = opts.get_option( "PARTITION", partition_tag_name );
 if( result == MB_SUCCESS ) mPartitionTagName = partition_tag_name;
 
 FILE* file = fopen( filename, "r" );
 if( !file ) return MB_FILE_DOES_NOT_EXIST;
 
 // Read file header
 
 if( !fgets( vendor_string, sizeof( vendor_string ), file ) )
 {
 fclose( file );
 return MB_FAILURE;
 }
 
 if( !strchr( vendor_string, '\n' ) || 2 != sscanf( vendor_string, "# vtk DataFile Version %d.%d", &major, &minor ) )
 {
 fclose( file );
 return MB_FAILURE;
 }
 
 if( !fgets( vendor_string, sizeof( vendor_string ), file ) )
 {
 fclose( file );
 return MB_FAILURE;
 }
 
 // VTK spec says this should not exceed 256 chars.
 if( !strchr( vendor_string, '\n' ) )
 {
 fclose( file );
 MB_SET_ERR( MB_FAILURE, "Vendor string (line 2) exceeds 256 characters" );
 }
 
 // Check file type
 
 FileTokenizer tokens( file, readMeshIface );
 const char* const file_type_names[] = { "ASCII", "BINARY", 0 };
 int filetype = tokens.match_token( file_type_names );
 switch( filetype )
 {
 case 2: // BINARY
 MB_SET_ERR( MB_FAILURE, "Cannot read BINARY VTK files" );
 default: // ERROR
 return MB_FAILURE;
 case 1: // ASCII
 break;
 }
 
 // Read the mesh
 if( !tokens.match_token( "DATASET" ) ) return MB_FAILURE;
 result = vtk_read_dataset( tokens, vertices, element_list );
 if( MB_SUCCESS != result ) return result;
 
 if( file_id_tag )
 {
 result = store_file_ids( *file_id_tag, vertices, element_list );
 if( MB_SUCCESS != result ) return result;
 }
 
 // Count the number of elements read
 long elem_count = 0;
 for( std::vector< Range >::iterator it = element_list.begin(); it != element_list.end(); ++it )
 elem_count += it->size();
 
 // Read attribute data until end of file.
 const char* const block_type_names[] = { "POINT_DATA", "CELL_DATA", 0 };
 std::vector< Range > vertex_list( 1 );
 vertex_list[0] = vertices;
 int blocktype = 0;
 while( !tokens.eof() )
 {
 // Get POINT_DATA or CELL_DATA
 int new_block_type = tokens.match_token( block_type_names, false );
 if( tokens.eof() ) break;
 
 if( !new_block_type )
 {
 // If next token was neither POINT_DATA nor CELL_DATA,
 // then there's another attribute under the current one.
 if( blocktype )
 tokens.unget_token();
 else
 break;
 }
 else
 {
 blocktype = new_block_type;
 long count;
 if( !tokens.get_long_ints( 1, &count ) ) return MB_FAILURE;
 
 if( blocktype == 1 && (unsigned long)count != vertices.size() )
 {
 MB_SET_ERR( MB_FAILURE, "Count inconsistent with number of vertices at line " << tokens.line_number() );
 }
 else if( blocktype == 2 && count != elem_count )
 {
 MB_SET_ERR( MB_FAILURE, "Count inconsistent with number of elements at line " << tokens.line_number() );
 }
 }
 
 if( blocktype == 1 )
 result = vtk_read_attrib_data( tokens, vertex_list );
 else
 result = vtk_read_attrib_data( tokens, element_list );
 
 if( MB_SUCCESS != result ) return result;
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::allocate_vertices( long num_verts,
 EntityHandle& start_handle_out,
 double*& x_coord_array_out,
 double*& y_coord_array_out,
 double*& z_coord_array_out )
{
 ErrorCode result;
 
 // Create vertices
 std::vector< double* > arrays;
 start_handle_out = 0;
 result = readMeshIface->get_node_coords( 3, num_verts, MB_START_ID, start_handle_out, arrays );
 if( MB_SUCCESS != result ) return result;
 
 x_coord_array_out = arrays[0];
 y_coord_array_out = arrays[1];
 z_coord_array_out = arrays[2];
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::read_vertices( FileTokenizer& tokens, long num_verts, EntityHandle& start_handle_out )
{
 ErrorCode result;
 double *x, *y, *z;
 
 result = allocate_vertices( num_verts, start_handle_out, x, y, z );
 if( MB_SUCCESS != result ) return result;
 
 // Read vertex coordinates
 for( long vtx = 0; vtx < num_verts; ++vtx )
 {
 if( !tokens.get_doubles( 1, x++ ) || !tokens.get_doubles( 1, y++ ) || !tokens.get_doubles( 1, z++ ) )
 return MB_FAILURE;
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::allocate_elements( long num_elements,
 int vert_per_element,
 EntityType type,
 EntityHandle& start_handle_out,
 EntityHandle*& conn_array_out,
 std::vector< Range >& append_to_this )
{
 ErrorCode result;
 
 start_handle_out = 0;
 result = readMeshIface->get_element_connect( num_elements, vert_per_element, type, MB_START_ID, start_handle_out,
 conn_array_out );
 if( MB_SUCCESS != result ) return result;
 
 Range range( start_handle_out, start_handle_out + num_elements - 1 );
 append_to_this.push_back( range );
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_read_dataset( FileTokenizer& tokens, Range& vertex_list, std::vector< Range >& element_list )
{
 const char* const data_type_names[] = {
 "STRUCTURED_POINTS", "STRUCTURED_GRID", "UNSTRUCTURED_GRID", "POLYDATA", "RECTILINEAR_GRID", "FIELD", 0 };
 int datatype = tokens.match_token( data_type_names );
 switch( datatype )
 {
 case 1:
 return vtk_read_structured_points( tokens, vertex_list, element_list );
 case 2:
 return vtk_read_structured_grid( tokens, vertex_list, element_list );
 case 3:
 return vtk_read_unstructured_grid( tokens, vertex_list, element_list );
 case 4:
 return vtk_read_polydata( tokens, vertex_list, element_list );
 case 5:
 return vtk_read_rectilinear_grid( tokens, vertex_list, element_list );
 case 6:
 return vtk_read_field( tokens );
 default:
 return MB_FAILURE;
 }
}
 
ErrorCode ReadVtk::vtk_read_structured_points( FileTokenizer& tokens,
 Range& vertex_list,
 std::vector< Range >& elem_list )
{
 long i, j, k;
 long dims[3];
 double origin[3], space[3];
 ErrorCode result;
 
 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
 }
 
 if( !tokens.match_token( "ORIGIN" ) || !tokens.get_doubles( 3, origin ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 const char* const spacing_names[] = { "SPACING", "ASPECT_RATIO", 0 };
 if( !tokens.match_token( spacing_names ) || !tokens.get_doubles( 3, space ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 // Create vertices
 double *x, *y, *z;
 EntityHandle start_handle = 0;
 long num_verts = dims[0] * dims[1] * dims[2];
 result = allocate_vertices( num_verts, start_handle, x, y, z );
 if( MB_SUCCESS != result ) return result;
 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
 
 for( k = 0; k < dims[2]; ++k )
 for( j = 0; j < dims[1]; ++j )
 for( i = 0; i < dims[0]; ++i )
 {
 *x = origin[0] + i * space[0];
 ++x;
 *y = origin[1] + j * space[1];
 ++y;
 *z = origin[2] + k * space[2];
 ++z;
 }
 
 return vtk_create_structured_elems( dims, start_handle, elem_list );
}
 
ErrorCode ReadVtk::vtk_read_structured_grid( FileTokenizer& tokens,
 Range& vertex_list,
 std::vector< Range >& elem_list )
{
 long num_verts, dims[3];
 ErrorCode result;
 
 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
 }
 
 if( !tokens.match_token( "POINTS" ) || !tokens.get_long_ints( 1, &num_verts ) ||
 !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( num_verts != ( dims[0] * dims[1] * dims[2] ) )
 {
 MB_SET_ERR( MB_FAILURE, "Point count not consistent with dimensions at line " << tokens.line_number() );
 }
 
 // Create and read vertices
 EntityHandle start_handle = 0;
 result = read_vertices( tokens, num_verts, start_handle );
 if( MB_SUCCESS != result ) return result;
 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
 
 return vtk_create_structured_elems( dims, start_handle, elem_list );
}
 
ErrorCode ReadVtk::vtk_read_rectilinear_grid( FileTokenizer& tokens,
 Range& vertex_list,
 std::vector< Range >& elem_list )
{
 int i, j, k;
 long dims[3];
 const char* labels[] = { "X_COORDINATES", "Y_COORDINATES", "Z_COORDINATES" };
 std::vector< double > coords[3];
 ErrorCode result;
 
 if( !tokens.match_token( "DIMENSIONS" ) || !tokens.get_long_ints( 3, dims ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( dims[0] < 1 || dims[1] < 1 || dims[2] < 1 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid dimension at line " << tokens.line_number() );
 }
 
 for( i = 0; i < 3; i++ )
 {
 long count;
 if( !tokens.match_token( labels[i] ) || !tokens.get_long_ints( 1, &count ) ||
 !tokens.match_token( vtk_type_names ) )
 return MB_FAILURE;
 
 if( count != dims[i] )
 {
 MB_SET_ERR( MB_FAILURE, "Coordinate count inconsistent with dimensions at line " << tokens.line_number() );
 }
 
 coords[i].resize( count );
 if( !tokens.get_doubles( count, &coords[i][0] ) ) return MB_FAILURE;
 }
 
 // Create vertices
 double *x, *y, *z;
 EntityHandle start_handle = 0;
 long num_verts = dims[0] * dims[1] * dims[2];
 result = allocate_vertices( num_verts, start_handle, x, y, z );
 if( MB_SUCCESS != result ) return result;
 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
 
 // Calculate vertex coordinates
 for( k = 0; k < dims[2]; ++k )
 for( j = 0; j < dims[1]; ++j )
 for( i = 0; i < dims[0]; ++i )
 {
 *x = coords[0][i];
 ++x;
 *y = coords[1][j];
 ++y;
 *z = coords[2][k];
 ++z;
 }
 
 return vtk_create_structured_elems( dims, start_handle, elem_list );
}
 
ErrorCode ReadVtk::vtk_read_polydata( FileTokenizer& tokens, Range& vertex_list, std::vector< Range >& elem_list )
{
 ErrorCode result;
 long num_verts;
 const char* const poly_data_names[] = { "VERTICES", "LINES", "POLYGONS", "TRIANGLE_STRIPS", 0 };
 
 if( !tokens.match_token( "POINTS" ) || !tokens.get_long_ints( 1, &num_verts ) ||
 !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( num_verts < 1 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid point count at line " << tokens.line_number() );
 }
 
 // Create vertices and read coordinates
 EntityHandle start_handle = 0;
 result = read_vertices( tokens, num_verts, start_handle );
 if( MB_SUCCESS != result ) return result;
 vertex_list.insert( start_handle, start_handle + num_verts - 1 );
 
 int poly_type = tokens.match_token( poly_data_names );
 switch( poly_type )
 {
 case 0:
 result = MB_FAILURE;
 break;
 case 1:
 MB_SET_ERR( MB_FAILURE, "Vertex element type at line " << tokens.line_number() );
 break;
 case 2:
 MB_SET_ERR( MB_FAILURE, "Unsupported type: polylines at line " << tokens.line_number() );
 result = MB_FAILURE;
 break;
 case 3:
 result = vtk_read_polygons( tokens, start_handle, elem_list );
 break;
 case 4:
 MB_SET_ERR( MB_FAILURE, "Unsupported type: triangle strips at line " << tokens.line_number() );
 result = MB_FAILURE;
 break;
 }
 
 return result;
}
 
ErrorCode ReadVtk::vtk_read_polygons( FileTokenizer& tokens, EntityHandle first_vtx, std::vector< Range >& elem_list )
{
 ErrorCode result;
 long size[2];
 
 if( !tokens.get_long_ints( 2, size ) || !tokens.get_newline() ) return MB_FAILURE;
 
 const Range empty;
 std::vector< EntityHandle > conn_hdl;
 std::vector< long > conn_idx;
 EntityHandle first = 0, prev = 0, handle;
 for( int i = 0; i < size[0]; ++i )
 {
 long count;
 if( !tokens.get_long_ints( 1, &count ) ) return MB_FAILURE;
 conn_idx.resize( count );
 conn_hdl.resize( count );
 if( !tokens.get_long_ints( count, &conn_idx[0] ) ) return MB_FAILURE;
 
 for( long j = 0; j < count; ++j )
 conn_hdl[j] = first_vtx + conn_idx[j];
 
 result = mdbImpl->create_element( MBPOLYGON, &conn_hdl[0], count, handle );
 if( MB_SUCCESS != result ) return result;
 
 if( prev + 1 != handle )
 {
 if( first )
 { // True except for first iteration (first == 0)
 if( elem_list.empty() || first < elem_list.back().front() ) // Only need new range if order would get
 // mixed up, or we just began inserting
 elem_list.push_back( empty );
 elem_list.back().insert( first, prev );
 }
 first = handle;
 }
 prev = handle;
 }
 if( first )
 { // True unless no elements (size[0] == 0)
 if( elem_list.empty() || first < elem_list.back().front() ) // Only need new range if order would get mixed
 // up, or we just began inserting
 elem_list.push_back( empty );
 elem_list.back().insert( first, prev );
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_read_unstructured_grid( FileTokenizer& tokens,
 Range& vertex_list,
 std::vector< Range >& elem_list )
{
 ErrorCode result;
 long i, num_verts, num_elems[2];
 EntityHandle tmp_conn_list[27];
 
 // Poorly formatted VTK legacy format document seems to
 // lead many to think that a FIELD block can occur within
 // an UNSTRUCTURED_GRID dataset rather than as its own data
 // set. So allow for field data between other blocks of
 // data.
 
 const char* pts_str[] = { "FIELD", "POINTS", 0 };
 while( 1 == ( i = tokens.match_token( pts_str ) ) )
 {
 result = vtk_read_field( tokens );
 if( MB_SUCCESS != result ) return result;
 }
 if( i != 2 ) return MB_FAILURE;
 
 if( !tokens.get_long_ints( 1, &num_verts ) || !tokens.match_token( vtk_type_names ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 if( num_verts < 1 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid point count at line " << tokens.line_number() );
 }
 
 // Create vertices and read coordinates
 EntityHandle first_vertex = 0;
 result = read_vertices( tokens, num_verts, first_vertex );
 if( MB_SUCCESS != result ) return result;
 vertex_list.insert( first_vertex, first_vertex + num_verts - 1 );
 
 const char* cell_str[] = { "FIELD", "CELLS", 0 };
 while( 1 == ( i = tokens.match_token( cell_str ) ) )
 {
 result = vtk_read_field( tokens );
 if( MB_SUCCESS != result ) return result;
 }
 if( i != 2 ) return MB_FAILURE;
 
 if( !tokens.get_long_ints( 2, num_elems ) || !tokens.get_newline() ) return MB_FAILURE;
 
 // Read element connectivity for all elements
 std::vector< long > connectivity( num_elems[1] );
 if( !tokens.get_long_ints( num_elems[1], &connectivity[0] ) ) return MB_FAILURE;
 
 if( !tokens.match_token( "CELL_TYPES" ) || !tokens.get_long_ints( 1, &num_elems[1] ) || !tokens.get_newline() )
 return MB_FAILURE;
 
 // Read element types
 std::vector< long > types( num_elems[0] );
 if( !tokens.get_long_ints( num_elems[0], &types[0] ) ) return MB_FAILURE;
 
 // Create elements in blocks of the same type
 // It is important to preserve the order in
 // which the elements were read for later reading
 // attribute data.
 long id = 0;
 std::vector< long >::iterator conn_iter = connectivity.begin();
 while( id < num_elems[0] )
 {
 unsigned vtk_type = types[id];
 if( vtk_type >= VtkUtil::numVtkElemType ) return MB_FAILURE;
 
 EntityType type = VtkUtil::vtkElemTypes[vtk_type].mb_type;
 if( type == MBMAXTYPE )
 {
 MB_SET_ERR( MB_FAILURE, "Unsupported VTK element type: " << VtkUtil::vtkElemTypes[vtk_type].name << " ("
 << vtk_type << ")" );
 }
 
 int num_vtx = *conn_iter;
 if( type != MBPOLYGON && type != MBPOLYHEDRON && num_vtx != (int)VtkUtil::vtkElemTypes[vtk_type].num_nodes )
 {
 MB_SET_ERR( MB_FAILURE, "Cell " << id << " is of type '" << VtkUtil::vtkElemTypes[vtk_type].name
 << "' but has " << num_vtx << " vertices" );
 }
 
 // Find any subsequent elements of the same type
 // if polyhedra, need to look at the number of faces to put in the same range
 std::vector< long >::iterator conn_iter2 = conn_iter + num_vtx + 1;
 long end_id = id + 1;
 if( MBPOLYHEDRON != type )
 {
 while( end_id < num_elems[0] && (unsigned)types[end_id] == vtk_type && *conn_iter2 == num_vtx )
 {
 ++end_id;
 conn_iter2 += num_vtx + 1;
 }
 }
 else
 {
 // advance only if next is polyhedron too, and if number of faces is the same
 int num_faces = conn_iter[1];
 while( end_id < num_elems[0] && (unsigned)types[end_id] == vtk_type && conn_iter2[1] == num_faces )
 {
 ++end_id;
 conn_iter2 += num_vtx + 1;
 }
 // num_vtx becomes in this case num_faces
 num_vtx = num_faces; // for polyhedra, this is what we want
 // trigger vertex adjacency call
 Range firstFaces;
 mdbImpl->get_adjacencies( &first_vertex, 1, 2, false, firstFaces );
 }
 
 // Allocate element block
 long num_elem = end_id - id;
 EntityHandle start_handle = 0;
 EntityHandle* conn_array;
 
 // if type is MBVERTEX, skip, we will not create elements with one vertex
 if( MBVERTEX == type )
 {
 id += num_elem;
 conn_iter += 2 * num_elem; // skip 2 * number of 1-vertex elements
 continue;
 }
 
 result = allocate_elements( num_elem, num_vtx, type, start_handle, conn_array, elem_list );
 if( MB_SUCCESS != result ) return result;
 
 EntityHandle* conn_sav = conn_array;
 
 // Store element connectivity
 if( type != MBPOLYHEDRON )
 {
 for( ; id < end_id; ++id )
 {
 if( conn_iter == connectivity.end() )
 {
 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at cell " << id );
 }
 // Make sure connectivity length is correct.
 if( *conn_iter != num_vtx )
 {
 MB_SET_ERR( MB_FAILURE, "Cell " << id << " is of type '" << VtkUtil::vtkElemTypes[vtk_type].name
 << "' but has " << num_vtx << " vertices" );
 }
 ++conn_iter;
 
 for( i = 0; i < num_vtx; ++i, ++conn_iter )
 {
 if( conn_iter == connectivity.end() )
 {
 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at cell " << id );
 }
 
 conn_array[i] = *conn_iter + first_vertex;
 }
 
 const unsigned* order = VtkUtil::vtkElemTypes[vtk_type].node_order;
 if( order )
 {
 assert( num_vtx * sizeof( EntityHandle ) <= sizeof( tmp_conn_list ) );
 memcpy( tmp_conn_list, conn_array, num_vtx * sizeof( EntityHandle ) );
 for( int j = 0; j < num_vtx; ++j )
 conn_array[order[j]] = tmp_conn_list[j];
 }
 
 conn_array += num_vtx;
 }
 }
 else // type == MBPOLYHEDRON
 {
 // in some cases, we may need to create new elements; will it screw the tags?
 // not if the file was not from moab
 ErrorCode rv = MB_SUCCESS;
 for( ; id < end_id; ++id )
 {
 if( conn_iter == connectivity.end() )
 {
 MB_SET_ERR( MB_FAILURE, "Connectivity data truncated at polyhedra cell " << id );
 }
 ++conn_iter;
 // iterator is now at number of faces
 // we should check it is indeed num_vtx
 int num_faces = *conn_iter;
 if( num_faces != num_vtx ) MB_SET_ERR( MB_FAILURE, "Connectivity data wrong at polyhedra cell " << id );
 
 EntityHandle connec[20]; // we bet we will have only 20 vertices at most, in a
 // face in a polyhedra
 for( int j = 0; j < num_faces; j++ )
 {
 conn_iter++;
 int numverticesInFace = (int)*conn_iter;
 if( numverticesInFace > 20 )
 MB_SET_ERR( MB_FAILURE,
 "too many vertices in face index " << j << " for polyhedra cell " << id );
 // need to find the face, but first fill with vertices
 for( int k = 0; k < numverticesInFace; k++ )
 {
 connec[k] = first_vertex + *( ++conn_iter ); //
 }
 Range adjFaces;
 // find a face with these vertices; if not, we need to create one, on the fly :(
 rv = mdbImpl->get_adjacencies( connec, numverticesInFace, 2, false, adjFaces );MB_CHK_ERR( rv );
 if( adjFaces.size() >= 1 )
 {
 conn_array[j] = adjFaces[0]; // get the first face found
 }
 else
 {
 // create the face; tri, quad or polygon
 EntityType etype = MBTRI;
 if( 4 == numverticesInFace ) etype = MBQUAD;
 if( 4 < numverticesInFace ) etype = MBPOLYGON;
 
 rv = mdbImpl->create_element( etype, connec, numverticesInFace, conn_array[j] );MB_CHK_ERR( rv );
 }
 }
 
 conn_array += num_vtx; // advance for next polyhedra
 conn_iter++; // advance to the next field
 }
 }
 
 // Notify MOAB of the new elements
 result = readMeshIface->update_adjacencies( start_handle, num_elem, num_vtx, conn_sav );
 if( MB_SUCCESS != result ) return result;
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_create_structured_elems( const long* dims,
 EntityHandle first_vtx,
 std::vector< Range >& elem_list )
{
 ErrorCode result;
 // int non_zero[3] = {0, 0, 0}; // True if dim > 0 for x, y, z respectively
 long elem_dim = 0; // Element dimension (2->quad, 3->hex)
 long num_elems = 1; // Total number of elements
 long vert_per_elem; // Element connectivity length
 long edims[3] = { 1, 1, 1 }; // Number of elements in each grid direction
 
 // Populate above data
 for( int d = 0; d < 3; d++ )
 {
 if( dims[d] > 1 )
 {
 // non_zero[elem_dim] = d;
 ++elem_dim;
 edims[d] = dims[d] - 1;
 num_elems *= edims[d];
 }
 }
 vert_per_elem = 1 << elem_dim;
 
 // Get element type from element dimension
 EntityType type;
 switch( elem_dim )
 {
 case 1:
 type = MBEDGE;
 break;
 case 2:
 type = MBQUAD;
 break;
 case 3:
 type = MBHEX;
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Invalid dimension for structured elements: " << elem_dim );
 }
 
 // Allocate storage for elements
 EntityHandle start_handle = 0;
 EntityHandle* conn_array;
 result = allocate_elements( num_elems, vert_per_elem, type, start_handle, conn_array, elem_list );
 if( MB_SUCCESS != result ) return MB_FAILURE;
 
 EntityHandle* conn_sav = conn_array;
 
 // Offsets of element vertices in grid relative to corner closest to origin
 long k = dims[0] * dims[1];
 const long corners[8] = { 0, 1, 1 + dims[0], dims[0], k, k + 1, k + 1 + dims[0], k + dims[0] };
 
 // Populate element list
 for( long z = 0; z < edims[2]; ++z )
 for( long y = 0; y < edims[1]; ++y )
 for( long x = 0; x < edims[0]; ++x )
 {
 const long index = x + y * dims[0] + z * ( dims[0] * dims[1] );
 for( long j = 0; j < vert_per_elem; ++j, ++conn_array )
 *conn_array = index + corners[j] + first_vtx;
 }
 
 // Notify MOAB of the new elements
 result = readMeshIface->update_adjacencies( start_handle, num_elems, vert_per_elem, conn_sav );
 if( MB_SUCCESS != result ) return result;
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_read_field( FileTokenizer& tokens )
{
 // This is not supported yet.
 // Parse the data but throw it away because
 // Mesquite has no internal representation for it.
 
 // Could save this in tags, but the only useful thing that
 // could be done with the data is to write it back out
 // with the modified mesh. As there's no way to save the
 // type of a tag in Mesquite, it cannot be written back
 // out correctly either.
 // FIXME: Don't know what to do with this data.
 // For now, read it and throw it out.
 
 long num_arrays;
 if( !tokens.get_string() || // Name
 !tokens.get_long_ints( 1, &num_arrays ) )
 return MB_FAILURE;
 
 for( long i = 0; i < num_arrays; ++i )
 {
 /*const char* name =*/tokens.get_string();
 
 long dims[2];
 if( !tokens.get_long_ints( 2, dims ) || !tokens.match_token( vtk_type_names ) ) return MB_FAILURE;
 
 long num_vals = dims[0] * dims[1];
 
 for( long j = 0; j < num_vals; j++ )
 {
 double junk;
 if( !tokens.get_doubles( 1, &junk ) ) return MB_FAILURE;
 }
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_read_attrib_data( FileTokenizer& tokens, std::vector< Range >& entities )
{
 const char* const type_names[] = { "SCALARS", "COLOR_SCALARS", "VECTORS", "NORMALS", "TEXTURE_COORDINATES",
 "TENSORS", "FIELD", 0 };
 
 int type = tokens.match_token( type_names );
 const char* tmp_name = tokens.get_string();
 if( !type || !tmp_name ) return MB_FAILURE;
 
 std::string name_alloc( tmp_name );
 const char* name = name_alloc.c_str();
 switch( type )
 {
 case 1:
 return vtk_read_scalar_attrib( tokens, entities, name );
 case 2:
 return vtk_read_color_attrib( tokens, entities, name );
 case 3:
 return vtk_read_vector_attrib( tokens, entities, name );
 case 4:
 return vtk_read_vector_attrib( tokens, entities, name );
 case 5:
 return vtk_read_texture_attrib( tokens, entities, name );
 case 6:
 return vtk_read_tensor_attrib( tokens, entities, name );
 case 7:
 return vtk_read_field_attrib( tokens, entities, name );
 }
 
 return MB_FAILURE;
}
 
ErrorCode ReadVtk::vtk_read_tag_data( FileTokenizer& tokens,
 int type,
 size_t per_elem,
 std::vector< Range >& entities,
 const char* name )
{
 ErrorCode result;
 DataType mb_type;
 if( type == 1 )
 {
 mb_type = MB_TYPE_BIT;
 }
 else if( type >= 2 && type <= 9 )
 {
 mb_type = MB_TYPE_INTEGER;
 }
 else if( type == 10 || type == 11 )
 {
 mb_type = MB_TYPE_DOUBLE;
 }
 else if( type == 12 )
 {
 mb_type = MB_TYPE_INTEGER;
 }
 else
 return MB_FAILURE;
 
#ifdef MB_VTK_MATERIAL_SETS
 size_t size;
 if( type == 1 )
 {
 size = sizeof( bool );
 }
 else if( type >= 2 && type <= 9 )
 {
 size = sizeof( int );
 }
 else if( type == 10 || type == 11 )
 {
 size = sizeof( double );
 }
 else /* (type == 12) */
 {
 size = 4; // Could be 4 or 8, but we don't know. Hope it's 4 because MOAB doesn't support
 // 64-bit ints.
 }
 Modulator materialMap( this->mdbImpl );
 result = materialMap.initialize( this->mPartitionTagName, mb_type, size, per_elem );MB_CHK_SET_ERR( result, "MaterialMap tag (" << this->mPartitionTagName << ") creation failed." );
 bool isMaterial = size * per_elem <= 4 && // Must have int-sized values (ParallelComm requires it)
 !this->mPartitionTagName.empty() && // Must have a non-empty field name...
 !strcmp( name, this->mPartitionTagName.c_str() ); // ... that matches our spec.
#endif // MB_VTK_MATERIAL_SETS
 
 // Get/create tag
 Tag handle;
 result = mdbImpl->tag_get_handle( name, per_elem, mb_type, handle, MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( result, "Tag name conflict for attribute \"" << name << "\" at line " << tokens.line_number() );
 
 std::vector< Range >::iterator iter;
 
 if( type == 1 )
 {
 for( iter = entities.begin(); iter != entities.end(); ++iter )
 {
 bool* data = new bool[iter->size() * per_elem];
 if( !tokens.get_booleans( per_elem * iter->size(), data ) )
 {
 delete[] data;
 return MB_FAILURE;
 }
 
 bool* data_iter = data;
 Range::iterator ent_iter = iter->begin();
 for( ; ent_iter != iter->end(); ++ent_iter )
 {
 unsigned char bits = 0;
 for( unsigned j = 0; j < per_elem; ++j, ++data_iter )
 bits |= (unsigned char)( *data_iter << j );
#ifdef MB_VTK_MATERIAL_SETS
 if( isMaterial ) materialMap.add_entity( *ent_iter, &bits, 1 );
#endif // MB_VTK_MATERIAL_SETS
 result = mdbImpl->tag_set_data( handle, &*ent_iter, 1, &bits );
 if( MB_SUCCESS != result )
 {
 delete[] data;
 return result;
 }
 }
 delete[] data;
 }
 }
 else if( ( type >= 2 && type <= 9 ) || type == 12 )
 {
 std::vector< int > data;
 for( iter = entities.begin(); iter != entities.end(); ++iter )
 {
 data.resize( iter->size() * per_elem );
 if( !tokens.get_integers( iter->size() * per_elem, &data[0] ) ) return MB_FAILURE;
#ifdef MB_VTK_MATERIAL_SETS
 if( isMaterial ) materialMap.add_entities( *iter, (unsigned char*)&data[0], per_elem * size );
#endif // MB_VTK_MATERIAL_SETS
 result = mdbImpl->tag_set_data( handle, *iter, &data[0] );
 if( MB_SUCCESS != result ) return result;
 }
 }
 else if( type == 10 || type == 11 )
 {
 std::vector< double > data;
 for( iter = entities.begin(); iter != entities.end(); ++iter )
 {
 data.resize( iter->size() * per_elem );
 if( !tokens.get_doubles( iter->size() * per_elem, &data[0] ) ) return MB_FAILURE;
#ifdef MB_VTK_MATERIAL_SETS
 if( isMaterial ) materialMap.add_entities( *iter, (unsigned char*)&data[0], per_elem * size );
#endif // MB_VTK_MATERIAL_SETS
 result = mdbImpl->tag_set_data( handle, *iter, &data[0] );
 if( MB_SUCCESS != result ) return result;
 }
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::vtk_read_scalar_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
{
 int type = tokens.match_token( vtk_type_names );
 if( !type ) return MB_FAILURE;
 
 long size;
 const char* tok = tokens.get_string();
 if( !tok ) return MB_FAILURE;
 
 const char* end = 0;
 size = strtol( tok, (char**)&end, 0 );
 if( *end )
 {
 size = 1;
 tokens.unget_token();
 }
 
 // VTK spec says cannot be greater than 4--do we care?
 if( size < 1 )
 { //|| size > 4)
 MB_SET_ERR( MB_FAILURE, "Scalar count out of range [1,4] at line " << tokens.line_number() );
 }
 
 if( !tokens.match_token( "LOOKUP_TABLE" ) || !tokens.match_token( "default" ) ) return MB_FAILURE;
 
 return vtk_read_tag_data( tokens, type, size, entities, name );
}
 
ErrorCode ReadVtk::vtk_read_color_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
{
 long size;
 if( !tokens.get_long_ints( 1, &size ) || size < 1 ) return MB_FAILURE;
 
 return vtk_read_tag_data( tokens, 10, size, entities, name );
}
 
ErrorCode ReadVtk::vtk_read_vector_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
{
 int type = tokens.match_token( vtk_type_names );
 if( !type ) return MB_FAILURE;
 
 return vtk_read_tag_data( tokens, type, 3, entities, name );
}
 
ErrorCode ReadVtk::vtk_read_texture_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
{
 int type, dim;
 if( !tokens.get_integers( 1, &dim ) || !( type = tokens.match_token( vtk_type_names ) ) ) return MB_FAILURE;
 
 if( dim < 1 || dim > 3 )
 {
 MB_SET_ERR( MB_FAILURE, "Invalid dimension (" << dim << ") at line " << tokens.line_number() );
 }
 
 return vtk_read_tag_data( tokens, type, dim, entities, name );
}
 
ErrorCode ReadVtk::vtk_read_tensor_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* name )
{
 int type = tokens.match_token( vtk_type_names );
 if( !type ) return MB_FAILURE;
 
 return vtk_read_tag_data( tokens, type, 9, entities, name );
}
 
ErrorCode ReadVtk::vtk_read_field_attrib( FileTokenizer& tokens, std::vector< Range >& entities, const char* )
{
 long num_fields;
 if( !tokens.get_long_ints( 1, &num_fields ) ) return MB_FAILURE;
 
 long i;
 for( i = 0; i < num_fields; ++i )
 {
 const char* tok = tokens.get_string();
 if( !tok ) return MB_FAILURE;
 
 std::string name_alloc( tok );
 
 long num_comp;
 if( !tokens.get_long_ints( 1, &num_comp ) ) return MB_FAILURE;
 
 long num_tuples;
 if( !tokens.get_long_ints( 1, &num_tuples ) ) return MB_FAILURE;
 
 int type = tokens.match_token( vtk_type_names );
 if( !type ) return MB_FAILURE;
 
 ErrorCode result = vtk_read_tag_data( tokens, type, num_comp, entities, name_alloc.c_str() );MB_CHK_SET_ERR( result, "Error reading data for field \"" << name_alloc << "\" (" << num_comp << " components, "
 << num_tuples << " tuples, type " << type
 << ") at line " << tokens.line_number() );
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadVtk::store_file_ids( Tag tag, const Range& verts, const std::vector< Range >& elems )
{
 ErrorCode rval;
 
 rval = readMeshIface->assign_ids( tag, verts );
 if( MB_SUCCESS != rval ) return rval;
 
 int id = 0;
 for( size_t i = 0; i < elems.size(); ++i )
 {
 rval = readMeshIface->assign_ids( tag, elems[i], id );
 id += elems[i].size();
 }
 
 return MB_SUCCESS;
}
 
} // namespace moab