Cppcheck report - MOAB: tools/skin.cpp

#include <iostream>
#include <set>
#include <limits>
#include <ctime>
#include <vector>
#include <cstdlib>
#include <cstdio>
#include <cassert>
#if !defined( _MSC_VER ) && !defined( __MINGW32__ )
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#endif
#include <fcntl.h>
#include "moab/Interface.hpp"
#include "MBTagConventions.hpp"
#include "moab/Core.hpp"
#include "moab/Range.hpp"
#include "moab/Skinner.hpp"
#include "moab/AdaptiveKDTree.hpp"
#include "moab/CN.hpp"

using namespace moab;

static void get_time_mem( double& tot_time, double& tot_mem );

// Different platforms follow different conventions for usage
#if !defined( _MSC_VER ) && !defined( __MINGW32__ )
#include <sys/resource.h>
#endif
#ifdef SOLARIS
extern "C" int getrusage( int, struct rusage* );
#ifndef RUSAGE_SELF
#include </usr/ucbinclude/sys/rusage.h>
#endif
#endif

const char DEFAULT_FIXED_TAG[] = "fixed";
const int MIN_EDGE_LEN_DENOM   = 4;

#define CHKERROR( A )                                                        \
    do                                                                       \
    {                                                                        \
        if( MB_SUCCESS != ( A ) )                                            \
        {                                                                    \
            std::cerr << "Internal error at line " << __LINE__ << std::endl; \
            return 3;                                                        \
        }                                                                    \
    } while( false )

static ErrorCode merge_duplicate_vertices( Interface&, double epsilon );
static ErrorCode min_edge_length( Interface&, double& result );

static void usage( const char* argv0, bool help = false )
{
    std::ostream& str = help ? std::cout : std::cerr;

    str << "Usage: " << argv0
        << " [-b <block_num> [-b ...] ] [-l] [-m] [-M <n>] [-p] [-s <sideset_num>] [-S] [-t|-T "
           "<name>] [-w] [-v|-V <n>]"
        << " <input_file> [<output_file>]" << std::endl;
    str << "Help : " << argv0 << " -h" << std::endl;
    if( !help ) exit( 1 );

    str << "Options: " << std::endl;
    str << "-a : Compute skin using vert-elem adjacencies (more memory, less time)." << std::endl;
    str << "-b <block_num> : Compute skin only for material set/block <block_num>." << std::endl;
    str << "-p : Print cpu & memory performance." << std::endl;
    str << "-s <sideset_num> : Put skin in neumann set/sideset <sideset_num>." << std::endl;
    str << "-S : Look for and use structured mesh information to speed up skinning." << std::endl;
    str << "-t : Set '" << DEFAULT_FIXED_TAG << "' tag on skin vertices." << std::endl;
    str << "-T <name> : Create tag with specified name and set to 1 on skin vertices." << std::endl;
    str << "-w : Write out whole mesh (otherwise just writes skin)." << std::endl;
    str << "-m : consolidate duplicate vertices" << std::endl;
    str << "-M <n> : consolidate duplicate vertices with specified tolerance. "
           "(Default: min_edge_length/"
        << MIN_EDGE_LEN_DENOM << ")" << std::endl;
    str << "-l : List total numbers of entities and vertices in skin." << std::endl;
    exit( 0 );
}

int main( int argc, char* argv[] )
{
    int i = 1;
    std::vector< int > matsets;
    int neuset_num = -1;
    bool write_tag = false, write_whole_mesh = false;
    bool print_perf         = false;
    bool use_vert_elem_adjs = false;
    bool merge_vertices     = false;
    double merge_epsilon    = -1;
    bool list_skin          = false;
    bool use_scd            = false;
    const char* fixed_tag   = DEFAULT_FIXED_TAG;
    const char *input_file = 0, *output_file = 0;

    bool no_more_flags = false;
    char* endptr       = 0;
    long block         = 0;  // initialize to eliminate compiler warning
    while( i < argc )
    {
        if( !no_more_flags && argv[i][0] == '-' )
        {
            const int f = i++;
            for( int j = 1; argv[f][j]; ++j )
            {
                switch( argv[f][j] )
                {
                    case 'a':
                        use_vert_elem_adjs = true;
                        break;
                    case 'p':
                        print_perf = true;
                        break;
                    case 't':
                        write_tag = true;
                        break;
                    case 'w':
                        write_whole_mesh = true;
                        break;
                    case 'm':
                        merge_vertices = true;
                        break;
                    case '-':
                        no_more_flags = true;
                        break;
                    case 'h':
                        usage( argv[0], true );
                        break;
                    case 'l':
                        list_skin = true;
                        break;
                    case 'S':
                        use_scd = true;
                        break;
                    case 'b':
                        if( i == argc || 0 >= ( block = strtol( argv[i], &endptr, 0 ) ) || *endptr )
                        {
                            std::cerr << "Expected positive integer following '-b' flag" << std::endl;
                            usage( argv[0] );
                        }
                        matsets.push_back( (int)block );
                        ++i;
                        break;
                    case 's':
                        if( i == argc || 0 >= ( neuset_num = strtol( argv[i], &endptr, 0 ) ) || *endptr )
                        {
                            std::cerr << "Expected positive integer following '-s' flag" << std::endl;
                            usage( argv[0] );
                        }
                        ++i;
                        break;
                    case 'T':
                        if( i == argc || argv[i][0] == '-' )
                        {
                            std::cerr << "Expected tag name following '-T' flag" << std::endl;
                            usage( argv[0] );
                        }
                        fixed_tag = argv[i++];
                        break;
                    case 'M':
                        if( i == argc || 0.0 > ( merge_epsilon = strtod( argv[i], &endptr ) ) || *endptr )
                        {
                            std::cerr << "Expected positive numeric value following '-M' flag" << std::endl;
                            usage( argv[0] );
                        }
                        merge_vertices = true;
                        ++i;
                        break;
                    default:
                        std::cerr << "Unrecognized flag: '" << argv[f][j] << "'" << std::endl;
                        usage( argv[0] );
                        break;
                }
            }
        }
        else if( input_file && output_file )
        {
            std::cerr << "Extra argument: " << argv[i] << std::endl;
            usage( argv[0] );
        }
        else if( input_file )
        {
            output_file = argv[i++];
        }
        else
        {
            input_file = argv[i++];
        }
    }

    if( !input_file )
    {
        std::cerr << "No input file specified" << std::endl;
        usage( argv[0] );
    }

    ErrorCode result;
    Core mbimpl;
    Interface* iface = &mbimpl;

    if( print_perf )
    {
        double tmp_time1, tmp_mem1;
        get_time_mem( tmp_time1, tmp_mem1 );
        std::cout << "Before reading: cpu time = " << tmp_time1 << ", memory = " << tmp_mem1 / 1.0e6 << "MB."
                  << std::endl;
    }

    // read input file
    result = iface->load_mesh( input_file );
    if( MB_SUCCESS != result )
    {
        std::cerr << "Failed to load \"" << input_file << "\"." << std::endl;
        return 2;
    }
    std::cerr << "Read \"" << input_file << "\"" << std::endl;
    if( print_perf )
    {
        double tmp_time2, tmp_mem2;
        get_time_mem( tmp_time2, tmp_mem2 );
        std::cout << "After reading: cpu time = " << tmp_time2 << ", memory = " << tmp_mem2 / 1.0e6 << "MB."
                  << std::endl;
    }

    if( merge_vertices )
    {
        if( merge_epsilon < 0.0 )
        {
            if( MB_SUCCESS != min_edge_length( *iface, merge_epsilon ) )
            {
                std::cerr << "Error determining minimum edge length" << std::endl;
                return 1;
            }
            merge_epsilon /= MIN_EDGE_LEN_DENOM;
        }
        if( MB_SUCCESS != merge_duplicate_vertices( *iface, merge_epsilon ) )
        {
            std::cerr << "Error merging duplicate vertices" << std::endl;
            return 1;
        }
    }

    // get entities of largest dimension
    int dim = 4;
    Range entities;
    while( entities.empty() && dim > 1 )
    {
        dim--;
        result = iface->get_entities_by_dimension( 0, dim, entities );CHKERROR( result );
    }

    Range skin_ents;
    Tag matset_tag = 0, neuset_tag = 0;
    result = iface->tag_get_handle( MATERIAL_SET_TAG_NAME, 1, MB_TYPE_INTEGER, matset_tag );
    if( MB_SUCCESS != result ) return 1;
    result = iface->tag_get_handle( NEUMANN_SET_TAG_NAME, 1, MB_TYPE_INTEGER, neuset_tag );
    if( MB_SUCCESS != result ) return 1;

    if( matsets.empty() )
        skin_ents = entities;
    else
    {
        // get all entities in the specified blocks
        if( 0 == matset_tag )
        {
            std::cerr << "Couldn't find any material sets in this mesh." << std::endl;
            return 1;
        }

        for( std::vector< int >::iterator vit = matsets.begin(); vit != matsets.end(); ++vit )
        {
            int this_matset             = *vit;
            const void* this_matset_ptr = &this_matset;
            Range this_range, ent_range;
            result =
                iface->get_entities_by_type_and_tag( 0, MBENTITYSET, &matset_tag, &this_matset_ptr, 1, this_range );
            if( MB_SUCCESS != result )
            {
                std::cerr << "Trouble getting material set #" << *vit << std::endl;
                return 1;
            }
            else if( this_range.empty() )
            {
                std::cerr << "Warning: couldn't find material set " << *vit << std::endl;
                continue;
            }

            result = iface->get_entities_by_dimension( *this_range.begin(), dim, ent_range, true );
            if( MB_SUCCESS != result ) continue;
            skin_ents.merge( ent_range );
        }
    }

    if( skin_ents.empty() )
    {
        std::cerr << "No entities for which to compute skin; exiting." << std::endl;
        return 1;
    }

    if( use_vert_elem_adjs )
    {
        // make a call which we know will generate vert-elem adjs
        Range dum_range;
        result = iface->get_adjacencies( &( *skin_ents.begin() ), 1, 1, false, dum_range );
        if( MB_SUCCESS != result ) return 1;
    }

    double tmp_time = 0.0, tmp_mem = 0.0;
    if( print_perf )
    {
        get_time_mem( tmp_time, tmp_mem );
        std::cout << "Before skinning: cpu time = " << tmp_time << ", memory = " << tmp_mem / 1.0e6 << "MB."
                  << std::endl;
    }

    // skin the mesh
    Range forward_lower, reverse_lower;
    Skinner tool( iface );
    if( use_scd )
        result = tool.find_skin( 0, skin_ents, false, forward_lower, NULL, false, true, true );
    else
        result = tool.find_skin( 0, skin_ents, false, forward_lower, &reverse_lower );
    Range boundary;
    boundary.merge( forward_lower );
    boundary.merge( reverse_lower );
    if( MB_SUCCESS != result || boundary.empty() )
    {
        std::cerr << "Mesh skinning failed." << std::endl;
        return 3;
    }

    if( list_skin )
    {
        Range skin_verts;
        result = iface->get_adjacencies( boundary, 0, true, skin_verts, Interface::UNION );<--- Variable 'result' is assigned a value that is never used.
        std::cout << "Skin has ";
        if( skin_ents.num_of_dimension( 3 ) )
            std::cout << boundary.num_of_dimension( 2 ) << " faces and ";
        else if( skin_ents.num_of_dimension( 2 ) )
            std::cout << boundary.num_of_dimension( 1 ) << " edges and ";
        std::cout << skin_verts.size() << " vertices." << std::endl;
    }
    if( write_tag )
    {
        // get tag handle
        Tag tag;
        int zero = 0;
        result   = iface->tag_get_handle( fixed_tag, 1, MB_TYPE_INTEGER, tag, MB_TAG_DENSE | MB_TAG_CREAT, &zero );CHKERROR( result );

        // Set tags
        std::vector< int > ones;
        Range bverts;
        result = iface->get_adjacencies( boundary, 0, false, bverts, Interface::UNION );
        if( MB_SUCCESS != result )
        {
            std::cerr << "Trouble getting vertices on boundary." << std::endl;
            return 1;
        }
        ones.resize( bverts.size(), 1 );
        result = iface->tag_set_data( tag, bverts, &ones[0] );CHKERROR( result );
    }

    if( -1 != neuset_num )
    {
        // create a neumann set with these entities
        if( 0 == neuset_tag )
        {
            result = iface->tag_get_handle( "NEUMANN_SET_TAG_NAME", 1, MB_TYPE_INTEGER, neuset_tag,
                                            MB_TAG_SPARSE | MB_TAG_CREAT );
            if( MB_SUCCESS != result || 0 == neuset_tag ) return 1;
        }

        // always create a forward neumann set, assuming we have something in the set
        EntityHandle forward_neuset = 0;
        result                      = iface->create_meshset( MESHSET_SET, forward_neuset );
        if( MB_SUCCESS != result || 0 == forward_neuset ) return 1;
        result = iface->tag_set_data( neuset_tag, &forward_neuset, 1, &neuset_num );
        if( MB_SUCCESS != result ) return 1;

        if( !forward_lower.empty() )
        {
            result = iface->add_entities( forward_neuset, forward_lower );
            if( MB_SUCCESS != result ) return 1;
        }
        if( !reverse_lower.empty() )
        {
            EntityHandle reverse_neuset = 1;
            result                      = iface->create_meshset( MESHSET_SET, reverse_neuset );
            if( MB_SUCCESS != result || 0 == forward_neuset ) return 1;

            result = iface->add_entities( reverse_neuset, reverse_lower );
            if( MB_SUCCESS != result ) return 1;
            Tag sense_tag;
            int dum_sense = 0;
            result        = iface->tag_get_handle( "SENSE", 1, MB_TYPE_INTEGER, sense_tag, MB_TAG_SPARSE | MB_TAG_CREAT,
                                                   &dum_sense );
            if( result != MB_SUCCESS ) return 1;
            int sense_val = -1;
            result        = iface->tag_set_data( neuset_tag, &reverse_neuset, 1, &sense_val );
            if( MB_SUCCESS != result ) return 0;
            result = iface->add_entities( forward_neuset, &reverse_neuset, 1 );
            if( MB_SUCCESS != result ) return 0;
        }
    }

    if( NULL != output_file && write_whole_mesh )
    {

        // write output file
        result = iface->write_mesh( output_file );
        if( MB_SUCCESS != result )
        {
            std::cerr << "Failed to write \"" << output_file << "\"." << std::endl;
            return 2;
        }
        std::cerr << "Wrote \"" << output_file << "\"" << std::endl;
    }
    else if( NULL != output_file )
    {
        // write only skin; write them as one set
        EntityHandle skin_set;
        result = iface->create_meshset( MESHSET_SET, skin_set );
        if( MB_SUCCESS != result ) return 1;
        result = iface->add_entities( skin_set, forward_lower );
        if( MB_SUCCESS != result ) return 1;
        result = iface->add_entities( skin_set, reverse_lower );
        if( MB_SUCCESS != result ) return 1;

        int dum = 10000;
        result  = iface->tag_set_data( matset_tag, &skin_set, 1, &dum );
        if( MB_SUCCESS != result ) return 1;

        result = iface->write_mesh( output_file, &skin_set, 1 );
        if( MB_SUCCESS != result )
        {
            std::cerr << "Failed to write \"" << output_file << "\"." << std::endl;
            return 2;
        }
        std::cerr << "Wrote \"" << output_file << "\"" << std::endl;
    }

    if( print_perf )
    {
        double tot_time, tot_mem;
        get_time_mem( tot_time, tot_mem );
        std::cout << "Total cpu time = " << tot_time << " seconds." << std::endl;
        std::cout << "Total skin cpu time = " << tot_time - tmp_time << " seconds." << std::endl;
        std::cout << "Total memory = " << tot_mem / 1024 << " MB." << std::endl;
        std::cout << "Total skin memory = " << ( tot_mem - tmp_mem ) / 1024 << " MB." << std::endl;
        std::cout << "Entities: " << std::endl;
        iface->list_entities( 0, 0 );
    }

    return 0;
}

#if defined( _MSC_VER ) || defined( __MINGW32__ )
void get_time_mem( double& tot_time, double& tot_mem )
{
    tot_time = (double)clock() / CLOCKS_PER_SEC;
    tot_mem  = 0;
}
#else
void get_time_mem( double& tot_time, double& tot_mem )
{
    struct rusage r_usage;
    getrusage( RUSAGE_SELF, &r_usage );
    double utime = (double)r_usage.ru_utime.tv_sec + ( (double)r_usage.ru_utime.tv_usec / 1.e6 );
    double stime = (double)r_usage.ru_stime.tv_sec + ( (double)r_usage.ru_stime.tv_usec / 1.e6 );
    tot_time     = utime + stime;
    tot_mem      = 0;
    if( 0 != r_usage.ru_maxrss )
    {
        tot_mem = (double)r_usage.ru_maxrss;
    }
    else
    {
        // this machine doesn't return rss - try going to /proc
        // print the file name to open
        char file_str[4096], dum_str[4096];
        int file_ptr = open( "/proc/self/stat", O_RDONLY );
        int file_len = read( file_ptr, file_str, sizeof( file_str ) - 1 );
        if( file_len <= 0 )
        {
            close( file_ptr );
            return;
        }

        close( file_ptr );
        file_str[file_len] = '\0';
        // read the preceding fields and the ones we really want...
        int dum_int;
        unsigned int dum_uint, vm_size, rss;
        int num_fields = sscanf( file_str,
<--- sscanf() without field width limits can crash with huge input data. [+]
sscanf() without field width limits can crash with huge input data. Add a field width specifier to fix this problem.

Sample program that can crash:

#include <stdio.h>
int main()
{
    char c[5];
    scanf("%s", c);
    return 0;
}

Typing in 5 or more characters may make the program crash. The correct usage here is 'scanf("%4s", c);', as the maximum field width does not include the terminating null byte.
Source: http://linux.die.net/man/3/scanf
Source: http://www.opensource.apple.com/source/xnu/xnu-1456.1.26/libkern/stdio/scanf.c
                                 "%d "                 // pid
                                 "%s "                 // comm
                                 "%c "                 // state
                                 "%d %d %d %d %d "     // ppid, pgrp, session, tty, tpgid
                                 "%u %u %u %u %u "     // flags, minflt, cminflt, majflt, cmajflt
                                 "%d %d %d %d %d %d "  // utime, stime, cutime, cstime, counter, priority
                                 "%u %u "              // timeout, itrealvalue
                                 "%d "                 // starttime
                                 "%u %u",              // vsize, rss
                                 &dum_int, dum_str, dum_str, &dum_int, &dum_int, &dum_int, &dum_int, &dum_int,
                                 &dum_uint, &dum_uint, &dum_uint, &dum_uint, &dum_uint, &dum_int, &dum_int, &dum_int,
                                 &dum_int, &dum_int, &dum_int, &dum_uint, &dum_uint, &dum_int, &vm_size, &rss );
        if( num_fields == 24 ) tot_mem = ( (double)vm_size );
    }
}
#endif

ErrorCode min_edge_length( Interface& moab, double& result )
{
    double sqr_result = std::numeric_limits< double >::max();

    ErrorCode rval;
    Range entities;
    rval = moab.get_entities_by_handle( 0, entities );
    if( MB_SUCCESS != rval ) return rval;
    Range::iterator i = entities.upper_bound( MBVERTEX );
    entities.erase( entities.begin(), i );
    i = entities.lower_bound( MBENTITYSET );
    entities.erase( i, entities.end() );

    std::vector< EntityHandle > storage;
    for( i = entities.begin(); i != entities.end(); ++i )
    {
        EntityType t = moab.type_from_handle( *i );
        const EntityHandle* conn;
        int conn_len, indices[2];
        rval = moab.get_connectivity( *i, conn, conn_len, true, &storage );
        if( MB_SUCCESS != rval ) return rval;

        int num_edges = CN::NumSubEntities( t, 1 );
        for( int j = 0; j < num_edges; ++j )
        {
            CN::SubEntityVertexIndices( t, 1, j, indices );
            EntityHandle v[2] = { conn[indices[0]], conn[indices[1]] };
            if( v[0] == v[1] ) continue;

            double c[6];
            rval = moab.get_coords( v, 2, c );
            if( MB_SUCCESS != rval ) return rval;

            c[0] -= c[3];
            c[1] -= c[4];
            c[2] -= c[5];
            double len_sqr = c[0] * c[0] + c[1] * c[1] + c[2] * c[2];
            if( len_sqr < sqr_result ) sqr_result = len_sqr;
        }
    }

    result = sqrt( sqr_result );
    return MB_SUCCESS;
}

ErrorCode merge_duplicate_vertices( Interface& moab, const double epsilon )
{
    ErrorCode rval;
    Range verts;
    rval = moab.get_entities_by_type( 0, MBVERTEX, verts );
    if( MB_SUCCESS != rval ) return rval;

    AdaptiveKDTree tree( &moab );
    EntityHandle root;
    rval = tree.build_tree( verts, &root );
    if( MB_SUCCESS != rval )
    {
        fprintf( stderr, "Failed to build kD-tree.\n" );
        return rval;
    }

    std::set< EntityHandle > dead_verts;
    std::vector< EntityHandle > leaves;
    for( Range::iterator i = verts.begin(); i != verts.end(); ++i )
    {
        double coords[3];
        rval = moab.get_coords( &*i, 1, coords );
        if( MB_SUCCESS != rval ) return rval;

        leaves.clear();
        ;
        rval = tree.distance_search( coords, epsilon, leaves, epsilon, epsilon );
        if( MB_SUCCESS != rval ) return rval;

        Range near;
        for( std::vector< EntityHandle >::iterator j = leaves.begin(); j != leaves.end(); ++j )
        {
            Range tmp;
            rval = moab.get_entities_by_type( *j, MBVERTEX, tmp );
            if( MB_SUCCESS != rval ) return rval;
            near.merge( tmp.begin(), tmp.end() );
        }

        Range::iterator v = near.find( *i );
        assert( v != near.end() );
        near.erase( v );

        EntityHandle merge = 0;
        for( Range::iterator j = near.begin(); j != near.end(); ++j )
        {
            if( *j < *i && dead_verts.find( *j ) != dead_verts.end() ) continue;

            double coords2[3];
            rval = moab.get_coords( &*j, 1, coords2 );
            if( MB_SUCCESS != rval ) return rval;

            coords2[0] -= coords[0];
            coords2[1] -= coords[1];
            coords2[2] -= coords[2];
            double dsqr = coords2[0] * coords2[0] + coords2[1] * coords2[1] + coords2[2] * coords2[2];
            if( dsqr <= epsilon * epsilon )
            {
                merge = *j;
                break;
            }
        }

        if( merge )
        {
            dead_verts.insert( *i );
            rval = moab.merge_entities( merge, *i, false, true );
            if( MB_SUCCESS != rval ) return rval;
        }
    }

    if( dead_verts.empty() )
        std::cout << "No duplicate/coincident vertices." << std::endl;
    else
        std::cout << "Merged and deleted " << dead_verts.size() << " vertices "
                  << "coincident within " << epsilon << std::endl;

    return MB_SUCCESS;
}