Cppcheck report - MOAB: src/io/WriteVtk.cpp

/**
 * 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.
 *
 */

#ifdef WIN32
#ifdef _DEBUG
// turn off warnings that say they debugging identifier has been truncated
// this warning comes up when using some STL containers
#pragma warning( disable : 4786 )
#endif
#endif

#include "WriteVtk.hpp"
#include "moab/VtkUtil.hpp"
#include "SysUtil.hpp"

#include <fstream>
#include <iostream>
#include <cstdio>
#include <cassert>
#include <vector>
#include <set>
#include <map>
#include <iterator>

#include "moab/Interface.hpp"
#include "moab/Range.hpp"
#include "moab/CN.hpp"
#include "MBTagConventions.hpp"
#include "moab/WriteUtilIface.hpp"
#include "Internals.hpp"
#include "moab/FileOptions.hpp"

#define INS_ID( stringvar, prefix, id ) sprintf( stringvar, prefix, id )

namespace moab
{

const int DEFAULT_PRECISION = 10;
const bool DEFAULT_STRICT   = true;

WriterIface* WriteVtk::factory( Interface* iface )
{
    return new WriteVtk( iface );
}

WriteVtk::WriteVtk( Interface* impl )
    : mbImpl( impl ), writeTool( 0 ), mStrict( DEFAULT_STRICT ), freeNodes( 0 ), createOneNodeCells( false )
{
    assert( impl != NULL );
    impl->query_interface( writeTool );
}

WriteVtk::~WriteVtk()
{
    mbImpl->release_interface( writeTool );
}

ErrorCode WriteVtk::write_file( const char* file_name,
                                const bool overwrite,
                                const FileOptions& opts,
                                const EntityHandle* output_list,
                                const int num_sets,
                                const std::vector< std::string >& /* qa_list */,
                                const Tag* tag_list,
                                int num_tags,
                                int /* export_dimension */ )
{
    ErrorCode rval;

    // Get precision for node coordinates
    int precision;
    if( MB_SUCCESS != opts.get_int_option( "PRECISION", precision ) ) precision = DEFAULT_PRECISION;

    if( MB_SUCCESS == opts.get_null_option( "STRICT" ) )
        mStrict = true;
    else if( MB_SUCCESS == opts.get_null_option( "RELAXED" ) )
        mStrict = false;
    else
        mStrict = DEFAULT_STRICT;

    if( MB_SUCCESS == opts.get_null_option( "CREATE_ONE_NODE_CELLS" ) ) createOneNodeCells = true;

    // Get entities to write
    Range nodes, elems;
    rval = gather_mesh( output_list, num_sets, nodes, elems );
    if( MB_SUCCESS != rval ) return rval;

    // Honor overwrite flag
    if( !overwrite )
    {
        rval = writeTool->check_doesnt_exist( file_name );
        if( MB_SUCCESS != rval ) return rval;
    }

    // Create file
    std::ofstream file( file_name );
    if( !file )
    {
        MB_SET_ERR( MB_FILE_WRITE_ERROR, "Could not open file: " << file_name );
    }
    file.precision( precision );

    // Write file
    if( ( rval = write_header( file ) ) != MB_SUCCESS || ( rval = write_nodes( file, nodes ) ) != MB_SUCCESS ||
        ( rval = write_elems( file, nodes, elems ) ) != MB_SUCCESS ||
        ( rval = write_tags( file, true, nodes, tag_list, num_tags ) ) != MB_SUCCESS ||
        ( rval = write_tags( file, false, elems, tag_list, num_tags ) ) != MB_SUCCESS )
    {
        file.close();
        remove( file_name );
        return rval;
    }

    return MB_SUCCESS;
}

ErrorCode WriteVtk::gather_mesh( const EntityHandle* set_list, int num_sets, Range& nodes, Range& elems )
{
    ErrorCode rval;
    int e;

    if( !set_list || !num_sets )
    {
        Range a;
        rval = mbImpl->get_entities_by_handle( 0, a );
        if( MB_SUCCESS != rval ) return rval;

        Range::const_iterator node_i, elem_i, set_i;
        node_i = a.lower_bound( a.begin(), a.end(), CREATE_HANDLE( MBVERTEX, 0, e ) );
        elem_i = a.lower_bound( node_i, a.end(), CREATE_HANDLE( MBEDGE, 0, e ) );
        set_i  = a.lower_bound( elem_i, a.end(), CREATE_HANDLE( MBENTITYSET, 0, e ) );
        nodes.merge( node_i, elem_i );
        elems.merge( elem_i, set_i );

        // Filter out unsupported element types
        EntityType et = MBEDGE;
        for( et++; et < MBENTITYSET; et++ )
        {
            if( VtkUtil::get_vtk_type( et, CN::VerticesPerEntity( et ) ) ) continue;
            Range::iterator eit   = elems.lower_bound( elems.begin(), elems.end(), CREATE_HANDLE( et, 0, e ) ),
                            ep1it = elems.lower_bound( elems.begin(), elems.end(), CREATE_HANDLE( et + 1, 0, e ) );
            elems.erase( eit, ep1it );
        }
    }
    else
    {
        std::set< EntityHandle > visited;
        std::vector< EntityHandle > sets;
        sets.reserve( num_sets );
        std::copy( set_list, set_list + num_sets, std::back_inserter( sets ) );
        while( !sets.empty() )
        {
            // Get next set
            EntityHandle set = sets.back();
            sets.pop_back();
            // Skip sets we've already done
            if( !visited.insert( set ).second ) continue;

            Range a;
            rval = mbImpl->get_entities_by_handle( set, a );
            if( MB_SUCCESS != rval ) return rval;

            Range::const_iterator node_i, elem_i, set_i;
            node_i = a.lower_bound( a.begin(), a.end(), CREATE_HANDLE( MBVERTEX, 0, e ) );
            elem_i = a.lower_bound( node_i, a.end(), CREATE_HANDLE( MBEDGE, 0, e ) );
            set_i  = a.lower_bound( elem_i, a.end(), CREATE_HANDLE( MBENTITYSET, 0, e ) );
            nodes.merge( node_i, elem_i );
            elems.merge( elem_i, set_i );
            std::copy( set_i, a.end(), std::back_inserter( sets ) );

            a.clear();
            rval = mbImpl->get_child_meshsets( set, a );
            std::copy( a.begin(), a.end(), std::back_inserter( sets ) );
        }

        for( Range::const_iterator ei = elems.begin(); ei != elems.end(); ++ei )
        {
            std::vector< EntityHandle > connect;
            rval = mbImpl->get_connectivity( &( *ei ), 1, connect );
            if( MB_SUCCESS != rval ) return rval;

            for( unsigned int i = 0; i < connect.size(); ++i )
                nodes.insert( connect[i] );
        }
    }

    if( nodes.empty() )
    {
        MB_SET_ERR( MB_ENTITY_NOT_FOUND, "Nothing to write" );
    }

    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_header( std::ostream& stream )
{
    stream << "# vtk DataFile Version 3.0" << std::endl;
    stream << MOAB_VERSION_STRING << std::endl;
    stream << "ASCII" << std::endl;
    stream << "DATASET UNSTRUCTURED_GRID" << std::endl;
    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_nodes( std::ostream& stream, const Range& nodes )
{
    ErrorCode rval;

    stream << "POINTS " << nodes.size() << " double" << std::endl;

    double coords[3];
    for( Range::const_iterator i = nodes.begin(); i != nodes.end(); ++i )
    {
        coords[1] = coords[2] = 0.0;
        rval                  = mbImpl->get_coords( &( *i ), 1, coords );
        if( MB_SUCCESS != rval ) return rval;
        stream << coords[0] << ' ' << coords[1] << ' ' << coords[2] << std::endl;
    }

    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_elems( std::ostream& stream, const Range& nodes, const Range& elems )
{
    ErrorCode rval;

    Range connectivity;  // because we now support polyhedra, it could contain faces
    rval = mbImpl->get_connectivity( elems, connectivity );MB_CHK_ERR( rval );

    Range nodes_from_connectivity = connectivity.subset_by_type( MBVERTEX );
    Range faces_from_connectivity =
        subtract( connectivity, nodes_from_connectivity );  // these could be faces of polyhedra

    Range connected_nodes;
    rval = mbImpl->get_connectivity( faces_from_connectivity, connected_nodes );MB_CHK_ERR( rval );
    connected_nodes.merge( nodes_from_connectivity );

    Range free_nodes = subtract( nodes, connected_nodes );

    // Get and write counts
    unsigned long num_elems, num_uses;
    num_elems = num_uses = elems.size();

    std::map< EntityHandle, int > sizeFieldsPolyhedra;

    for( Range::const_iterator i = elems.begin(); i != elems.end(); ++i )
    {
        EntityType type = mbImpl->type_from_handle( *i );
        if( !VtkUtil::get_vtk_type( type, CN::VerticesPerEntity( type ) ) ) continue;

        EntityHandle elem           = *i;
        const EntityHandle* connect = NULL;
        int conn_len                = 0;
        // Dummy storage vector for structured mesh "get_connectivity" function
        std::vector< EntityHandle > storage;
        rval = mbImpl->get_connectivity( elem, connect, conn_len, false, &storage );MB_CHK_ERR( rval );

        num_uses += conn_len;
        // if polyhedra, we will count the number of nodes in each face too
        if( TYPE_FROM_HANDLE( elem ) == MBPOLYHEDRON )
        {
            int numFields = 1;  // there will be one for number of faces; forgot about this one
            for( int j = 0; j < conn_len; j++ )
            {
                const EntityHandle* conn = NULL;
                int num_nd               = 0;
                rval                     = mbImpl->get_connectivity( connect[j], conn, num_nd );MB_CHK_ERR( rval );
                numFields += num_nd + 1;
            }
            sizeFieldsPolyhedra[elem] = numFields;  // will be used later, at writing
            num_uses += ( numFields - conn_len );
        }
    }
    freeNodes = (int)free_nodes.size();
    if( !createOneNodeCells ) freeNodes = 0;  // do not create one node cells
    stream << "CELLS " << num_elems + freeNodes << ' ' << num_uses + 2 * freeNodes << std::endl;

    // Write element connectivity
    std::vector< int > conn_data;
    std::vector< unsigned > vtk_types( elems.size() + freeNodes );
    std::vector< unsigned >::iterator t = vtk_types.begin();
    for( Range::const_iterator i = elems.begin(); i != elems.end(); ++i )
    {
        // Get type information for element
        EntityHandle elem = *i;
        EntityType type   = TYPE_FROM_HANDLE( elem );

        // Get element connectivity
        const EntityHandle* connect = NULL;
        int conn_len                = 0;
        // Dummy storage vector for structured mesh "get_connectivity" function
        std::vector< EntityHandle > storage;
        rval = mbImpl->get_connectivity( elem, connect, conn_len, false, &storage );MB_CHK_ERR( rval );

        // Get VTK type
        const VtkElemType* vtk_type = VtkUtil::get_vtk_type( type, conn_len );
        if( !vtk_type )
        {
            // Try connectivity with 1 fewer node
            vtk_type = VtkUtil::get_vtk_type( type, conn_len - 1 );
            if( vtk_type )
                conn_len--;
            else
            {
                MB_SET_ERR( MB_FAILURE, "Vtk file format does not support elements of type "
                                            << CN::EntityTypeName( type ) << " (" << (int)type << ") with " << conn_len
                                            << " nodes" );
            }
        }

        // Save VTK type index for later
        *t = vtk_type->vtk_type;
        ++t;

        if( type != MBPOLYHEDRON )
        {
            // Get IDs from vertex handles
            assert( conn_len > 0 );
            conn_data.resize( conn_len );
            for( int j = 0; j < conn_len; ++j )
                conn_data[j] = nodes.index( connect[j] );

            // Write connectivity list
            stream << conn_len;
            if( vtk_type->node_order )
                for( int k = 0; k < conn_len; ++k )
                    stream << ' ' << conn_data[vtk_type->node_order[k]];
            else
                for( int k = 0; k < conn_len; ++k )
                    stream << ' ' << conn_data[k];
            stream << std::endl;
        }
        else
        {
            // POLYHEDRON needs a special case, loop over faces to get nodes
            stream << sizeFieldsPolyhedra[elem] << " " << conn_len;
            for( int k = 0; k < conn_len; k++ )
            {
                EntityHandle face        = connect[k];
                const EntityHandle* conn = NULL;
                int num_nodes            = 0;
                rval                     = mbImpl->get_connectivity( face, conn, num_nodes );MB_CHK_ERR( rval );
                //        num_uses += num_nd + 1; // 1 for number of vertices in face
                conn_data.resize( num_nodes );
                for( int j = 0; j < num_nodes; ++j )
                    conn_data[j] = nodes.index( conn[j] );

                stream << ' ' << num_nodes;

                for( int j = 0; j < num_nodes; ++j )
                    stream << ' ' << conn_data[j];
            }
            stream << std::endl;
        }
    }

    if( createOneNodeCells )
        for( Range::const_iterator v = free_nodes.begin(); v != free_nodes.end(); ++v, ++t )
        {
            EntityHandle node = *v;
            stream << "1 " << nodes.index( node ) << std::endl;
            *t = 1;
        }

    // Write element types
    stream << "CELL_TYPES " << vtk_types.size() << std::endl;
    for( std::vector< unsigned >::const_iterator i = vtk_types.begin(); i != vtk_types.end(); ++i )
        stream << *i << std::endl;

    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_tags( std::ostream& stream,
                                bool nodes,
                                const Range& entities,
                                const Tag* tag_list,
                                int num_tags )
{
    ErrorCode rval;

    // The #$%@#$% MOAB interface does not have a function to retrieve
    // all entities with a tag, only all entities with a specified type
    // and tag. Define types to loop over depending on the if vertex
    // or element tag data is being written. It seems horribly inefficient
    // to have the implementation subdivide the results by type and have
    // to call that function once for each type just to recombine the results.
    // Unfortunately, there doesn't seem to be any other way.
    EntityType low_type, high_type;
    if( nodes )
    {
        low_type  = MBVERTEX;
        high_type = MBEDGE;
    }
    else
    {
        low_type  = MBEDGE;
        high_type = MBENTITYSET;
    }

    // Get all defined tags
    std::vector< Tag > tags;
    std::vector< Tag >::iterator i;
    rval = writeTool->get_tag_list( tags, tag_list, num_tags, false );
    if( MB_SUCCESS != rval ) return rval;

    // For each tag...
    bool entities_have_tags = false;
    for( i = tags.begin(); i != tags.end(); ++i )
    {
        // Skip tags holding entity handles -- no way to save them
        DataType dtype;
        rval = mbImpl->tag_get_data_type( *i, dtype );
        if( MB_SUCCESS != rval ) return rval;
        if( dtype == MB_TYPE_HANDLE ) continue;

        // If in strict mode, don't write tags that do not fit in any
        // attribute type (SCALAR : 1 to 4 values, VECTOR : 3 values, TENSOR : 9 values)
        if( mStrict )
        {
            int count;
            rval = mbImpl->tag_get_length( *i, count );
            if( MB_SUCCESS != rval ) return rval;
            if( count < 1 || ( count > 4 && count != 9 ) ) continue;
        }

        // Get subset of input entities that have the tag set
        Range tagged;
        for( EntityType type = low_type; type < high_type; ++type )
        {
            Range tmp_tagged;
            rval = mbImpl->get_entities_by_type_and_tag( 0, type, &( *i ), 0, 1, tmp_tagged );
            if( MB_SUCCESS != rval ) return rval;
            tmp_tagged = intersect( tmp_tagged, entities );
            tagged.merge( tmp_tagged );
        }

        // If any entities were tagged
        if( !tagged.empty() )
        {
            // If this is the first tag being written for the
            // entity type, write the label marking the beginning
            // of the tag data.
            if( !entities_have_tags )
            {
                entities_have_tags = true;
                if( nodes )
                    stream << "POINT_DATA " << entities.size() << std::endl;
                else
                    stream << "CELL_DATA " << entities.size() + freeNodes << std::endl;
            }

            // Write the tag
            rval = write_tag( stream, *i, entities, tagged );
            if( MB_SUCCESS != rval ) return rval;
        }
    }

    return MB_SUCCESS;
}

template < typename T >
void WriteVtk::write_data( std::ostream& stream, const std::vector< T >& data, unsigned vals_per_tag )
{
    typename std::vector< T >::const_iterator d = data.begin();
    const unsigned long n                       = data.size() / vals_per_tag;

    for( unsigned long i = 0; i < n; ++i )
    {
        for( unsigned j = 0; j < vals_per_tag; ++j, ++d )
        {
            if( sizeof( T ) == 1 )
                stream << (unsigned int)*d << ' ';
            else
                stream << *d << ' ';
        }
        stream << std::endl;
    }
}

// template <>
// void WriteVtk::write_data<unsigned char>(std::ostream& stream,
//                                         const std::vector<unsigned char>& data,
//                                         unsigned vals_per_tag)
//{
//  std::vector<unsigned char>::const_iterator d = data.begin();
//  const unsigned long n = data.size() / vals_per_tag;
//
//  for (unsigned long i = 0; i < n; ++i) {
//    for (unsigned j = 0; j < vals_per_tag; ++j, ++d)
//      stream << (unsigned int)*d << ' ';
//    stream << std::endl;
//  }
//}

template < typename T >
ErrorCode WriteVtk::write_tag( std::ostream& stream, Tag tag, const Range& entities, const Range& tagged, const int )
{
    ErrorCode rval;
    int addFreeNodes = 0;
    if( TYPE_FROM_HANDLE( entities[0] ) > MBVERTEX ) addFreeNodes = freeNodes;
    // we created freeNodes 1-node cells, so we have to augment cell data too
    // we know that the 1 node cells are added at the end, after all other cells;
    // so the default values will be set to those extra , artificial cells
    const unsigned long n = entities.size() + addFreeNodes;

    // Get tag properties

    std::string name;
    int vals_per_tag;
    if( MB_SUCCESS != mbImpl->tag_get_name( tag, name ) || MB_SUCCESS != mbImpl->tag_get_length( tag, vals_per_tag ) )
        return MB_FAILURE;

    // Get a tag value for each entity. Do this by initializing the
    // "data" vector with zero, and then filling in the values for
    // the entities that actually have the tag set.
    std::vector< T > data;
    data.resize( n * vals_per_tag, 0 );
    // If there is a default value for the tag, set the actual default value
    std::vector< T > def_value( vals_per_tag );
    rval = mbImpl->tag_get_default_value( tag, &( def_value[0] ) );
    if( MB_SUCCESS == rval ) SysUtil::setmem( &( data[0] ), &( def_value[0] ), vals_per_tag * sizeof( T ), n );

    Range::const_iterator t               = tagged.begin();
    typename std::vector< T >::iterator d = data.begin();
    for( Range::const_iterator i = entities.begin(); i != entities.end() && t != tagged.end(); ++i, d += vals_per_tag )
    {
        if( *i == *t )
        {
            ++t;
            rval = mbImpl->tag_get_data( tag, &( *i ), 1, &( *d ) );
            if( MB_SUCCESS != rval ) return rval;
        }
    }

    // Write the tag values, one entity per line.
    write_data( stream, data, vals_per_tag );

    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_bit_tag( std::ostream& stream, Tag tag, const Range& entities, const Range& tagged )
{
    ErrorCode rval;
    const unsigned long n = entities.size();

    // Get tag properties

    std::string name;
    int vals_per_tag;
    if( MB_SUCCESS != mbImpl->tag_get_name( tag, name ) || MB_SUCCESS != mbImpl->tag_get_length( tag, vals_per_tag ) )
        return MB_FAILURE;

    if( vals_per_tag > 8 )
    {
        MB_SET_ERR( MB_FAILURE, "Invalid tag size for bit tag \"" << name << "\"" );
    }

    // Get a tag value for each entity.
    // Get bits for each entity and unpack into
    // one integer in the 'data' array for each bit.
    // Initialize 'data' to zero because we will skip
    // those entities for which the tag is not set.
    std::vector< unsigned short > data;
    data.resize( n * vals_per_tag, 0 );
    Range::const_iterator t                   = tagged.begin();
    std::vector< unsigned short >::iterator d = data.begin();
    for( Range::const_iterator i = entities.begin(); i != entities.end() && t != tagged.end(); ++i )
    {
        if( *i == *t )
        {
            ++t;
            unsigned char value;
            rval = mbImpl->tag_get_data( tag, &( *i ), 1, &value );
            for( int j = 0; j < vals_per_tag; ++j, ++d )
                *d = (unsigned short)( value & ( 1 << j ) ? 1 : 0 );
<--- Clarify calculation precedence for '&' and '?'. [+]
Suspicious calculation. Please use parentheses to clarify the code. The code ''a&b?c:d'' should be written as either ''(a&b)?c:d'' or ''a&(b?c:d)''.
            if( MB_SUCCESS != rval ) return rval;
        }
        else
        {
            // If tag is not set for entity, skip values in array
            d += vals_per_tag;
        }
    }

    // Write the tag values, one entity per line.
    write_data( stream, data, vals_per_tag );

    return MB_SUCCESS;
}

ErrorCode WriteVtk::write_tag( std::ostream& s, Tag tag, const Range& entities, const Range& tagged )
{
    // Get tag properties
    std::string name;
    DataType type;
    int vals_per_tag;
    if( MB_SUCCESS != mbImpl->tag_get_name( tag, name ) || MB_SUCCESS != mbImpl->tag_get_length( tag, vals_per_tag ) ||
        MB_SUCCESS != mbImpl->tag_get_data_type( tag, type ) )
        return MB_FAILURE;

    // Skip tags of type ENTITY_HANDLE
    if( MB_TYPE_HANDLE == type ) return MB_FAILURE;

    // Now that we're past the point where the name would be used in
    // an error message, remove any spaces to conform to VTK file.
    for( std::string::iterator i = name.begin(); i != name.end(); ++i )
    {
        if( isspace( *i ) || iscntrl( *i ) ) *i = '_';
    }

    // Write the tag description
    if( 3 == vals_per_tag && MB_TYPE_DOUBLE == type )
        s << "VECTORS " << name << ' ' << VtkUtil::vtkTypeNames[type] << std::endl;
    else if( 9 == vals_per_tag )
        s << "TENSORS " << name << ' ' << VtkUtil::vtkTypeNames[type] << std::endl;
    else
        s << "SCALARS " << name << ' ' << VtkUtil::vtkTypeNames[type] << ' ' << vals_per_tag << std::endl
          << "LOOKUP_TABLE default" << std::endl;

    // Write the tag data
    switch( type )
    {
        case MB_TYPE_OPAQUE:
            return write_tag< unsigned char >( s, tag, entities, tagged, 0 );
        case MB_TYPE_INTEGER:
            return write_tag< int >( s, tag, entities, tagged, 0 );
        case MB_TYPE_DOUBLE:
            return write_tag< double >( s, tag, entities, tagged, 0 );
        case MB_TYPE_BIT:
            return write_bit_tag( s, tag, entities, tagged );
        default:
            return MB_FAILURE;
    }
}

}  // namespace moab