addConnec.cpp File Reference

Example demonstrating addition of connectivity to point cloud data for visualization. More...

#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
#include <cmath>
#include <sstream>

Include dependency graph for addConnec.cpp:

Go to the source code of this file.

Functions
int	main (int argc, char *argv[])

Detailed Description

Example demonstrating addition of connectivity to point cloud data for visualization.

This example shows how to:

• Load point cloud data from H5M files
• Match vertices between different meshes using global IDs
• Add 2D cell connectivity to point cloud data
• Create new mesh files with enhanced connectivity
• Handle different element types (triangles, quads, polygons)
• Write enhanced meshes for better visualization

This tool is useful for converting point cloud data into connected meshes for better visualization in tools like VisIt.

Author

MOAB Development Team

Date

2024

this tool will take an existing h5m fine point cloud data (phys grid or land pc) and add 2d cells from a fine atm mesh

example of usage: ./addConnec -i wholeFineATM.h5m -s wholeLND_proj01.h5m -o wholeLndM.h5m

Basically, will output a new h5m file (wholeLndM.h5m), which has also cell connectivity copied from fine atm matching is based on the global ids between what we think is the order on the original file (wholeFineATM.h5m)

file wholeFineATM.h5m is obtained from a coupled run in e3sm, with the ne 11, np 4,

Parameters

argc	Number of command line arguments
argv	Command line arguments array

Returns

0 on success, 1 on failure

Definition in file addConnec.cpp.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 44 of file addConnec.cpp.

{
 
    ProgOptions opts;
 
    std::string inputfile, outfile( "out.h5m" ), sourcefile;
 
    opts.addOpt< std::string >( "input,i", "input mesh filename", &inputfile );
    opts.addOpt< std::string >( "source,s", "h5m file aligned with the mesh input file", &sourcefile );
    opts.addOpt< std::string >( "output,o", "output mesh filename", &outfile );
 
    opts.parseCommandLine( argc, argv );
 
    std::cout << "input mesh file: " << inputfile << "\n";
    std::cout << "source file: " << sourcefile << "\n";
    std::cout << "output file: " << outfile << "\n";
 
    if( inputfile.empty() )
    {
        opts.printHelp();
        return 0;
    }
    ErrorCode rval;
    Core* mb = new Core();
 
    MB_CHK_SET_ERR( mb->load_file( inputfile.c_str() ), "can't load input file" );
 
    Core* mb2 = new Core();
    MB_CHK_SET_ERR( mb2->load_file( sourcefile.c_str() ), "can't load source file" );
 
    // get vertices on ini mesh; get global id on ini mesh
    // get global id on source mesh
    Tag gid;
    Tag gid2;
    MB_CHK_SET_ERR( mb->tag_get_handle( "GLOBAL_ID", gid ), "can't get GLOBAL_ID tag on ini mesh " );
    MB_CHK_SET_ERR( mb2->tag_get_handle( "GLOBAL_ID", gid2 ), "can't get GLOBAL_ID tag on source mesh " );
 
    // get vertices on ini mesh; build
    Range iniVerts;
    MB_CHK_SET_ERR( mb->get_entities_by_dimension( 0, 0, iniVerts ), "can't get verts on initial mesh " );
 
    std::vector< int > gids;
    gids.resize( iniVerts.size() );
    MB_CHK_SET_ERR( mb->tag_get_data( gid, iniVerts, &( gids[0] ) ), "can't get gid on initial verts " );
    // build now the map
    std::map< int, EntityHandle > fromGidToEh;
    int i = 0;
    for( Range::iterator vit = iniVerts.begin(); vit != iniVerts.end(); ++vit, i++ )
    {
        fromGidToEh[gids[i]] = *vit;
    }
    // now get the source verts, and tags, and set it on new mesh
 
    Range sourceVerts;
    MB_CHK_SET_ERR( mb2->get_entities_by_dimension( 0, 0, sourceVerts ), "can't get verts on source mesh " );
    std::vector< int > gids2;
    gids2.resize( sourceVerts.size() );
    MB_CHK_SET_ERR( mb2->tag_get_data( gid2, sourceVerts, &( gids2[0] ) ), "can't get gid2 on cloud mesh " );
    std::map< int, EntityHandle > fromGid2ToEh;
    i = 0;
    for( Range::iterator vit = sourceVerts.begin(); vit != sourceVerts.end(); ++vit, i++ )
    {
        fromGid2ToEh[gids2[i]] = *vit;
    }
 
    Range usedVerts;
    for( size_t i = 0; i < gids2.size(); i++ )
    {
        int globalId          = gids2[i];
        EntityHandle usedVert = fromGidToEh[globalId];
        usedVerts.insert( usedVert );
    }
    Range cells;
    MB_CHK_SET_ERR( mb->get_adjacencies( usedVerts, 2, false, cells, Interface::UNION ), "can't get adj cells " );
 
    // now create a new cell in mb2 for each one in mb
    for( Range::iterator cit = cells.begin(); cit != cells.end(); ++cit )
    {
        EntityHandle cell        = *cit;
        int nnodes               = 0;
        const EntityHandle* conn = NULL;
        MB_CHK_SET_ERR( mb->get_connectivity( cell, conn, nnodes ), "can't get connectivity " );
 
        std::vector< EntityHandle > nconn( nnodes );
        bool goodCell = true;
        for( int i = 0; i < nnodes; i++ )
        {
            EntityHandle v = conn[i];
            int index      = iniVerts.index( v );
            if( index < 0 ) goodCell = false;
            int id = gids[index];
            if( fromGid2ToEh.find( id ) == fromGid2ToEh.end() )
                goodCell = false;
            else
                nconn[i] = fromGid2ToEh[id];
        }
        if( !goodCell ) continue;
        EntityType type = MBTRI;
        if( nnodes == 3 )
            type = MBTRI;
        else if( nnodes == 4 )
            type = MBQUAD;
        else if( nnodes > 4 )
            type = MBPOLYGON;
        EntityHandle nel;
        MB_CHK_SET_ERR( mb2->create_element( type, &nconn[0], nnodes, nel ), "can't create new cell " );
    }
    // save file
    MB_CHK_SET_ERR( mb2->write_file( outfile.c_str() ), "can't write file" );
 
    delete mb;
    delete mb2;
 
    return 0;
}

References ProgOptions::addOpt(), moab::Range::begin(), moab::Core::create_element(), moab::Range::end(), ErrorCode, moab::Core::get_adjacencies(), moab::Core::get_connectivity(), moab::Core::get_entities_by_dimension(), moab::index, moab::Range::index(), moab::Range::insert(), moab::Core::load_file(), mb, MB_CHK_SET_ERR, MBPOLYGON, MBQUAD, MBTRI, ProgOptions::parseCommandLine(), ProgOptions::printHelp(), moab::Range::size(), moab::Core::tag_get_data(), moab::Core::tag_get_handle(), moab::Interface::UNION, and moab::Core::write_file().