addPCdata.cpp File Reference

Example demonstrating addition of point cloud data to mesh files. More...

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

Include dependency graph for addPCdata.cpp:

Go to the source code of this file.

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

Detailed Description

Example demonstrating addition of point cloud data to mesh files.

This example shows how to:

• Load mesh files and point cloud data from H5M files
• Match entities between different meshes using global IDs
• Copy tag data from point cloud to mesh entities
• Handle different data types (integer, double)
• Support dual mesh operations for polygon data
• Create new mesh files with enhanced data
• Write enhanced meshes for visualization

This tool is useful for adding point cloud data to mesh files for better visualization and analysis in tools like VisIt.

Author

MOAB Development Team

Date

2024

this tool will take an existing h5m fine atm mesh file and add data from an h5m type file with point cloud mesh will support mainly showing the data with Visit

example of usage: ./mbaddpcdata -i wholeFineATM.h5m -s wholeLND_proj01.h5m -o atm_a2l.h5m -v a2lTbot_proj

it should work also for pentagon file style data ./mbaddpcdata -i MOABsource/MeshFiles/unittest/penta3d.h5m -s wholeLND_proj01.h5m -o atm_a2l.h5m -v a2lTbot_proj -p 1

Basically, will output a new h5m file (atm_a2l.h5m), which has an extra tag, corresponding to the variable a2lTbot_proj from the file wholeLND_proj01.h5m; matching is based on the global ids between what we think is the order on the original file (wholeFineATM.h5m) and the order of surfdata_ne11np4_simyr1850_c160614.nc

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 addPCdata.cpp.

Function Documentation

main()

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

Definition at line 50 of file addPCdata.cpp.

{
 
    ProgOptions opts;
 
    std::string inputfile, outfile( "out.h5m" ), sourcefile, variable_name;
    int dual_mesh = 0;
    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.addOpt< std::string >( "var,v", "variable to extract and add to output file", &variable_name );
    opts.addOpt< int >( "pentagon,p", "switch for dual mesh ", &dual_mesh );
 
    opts.parseCommandLine( argc, argv );
 
    std::cout << "input file: " << inputfile << "\n";
    std::cout << "source file: " << sourcefile << "\n";
    std::cout << "variable to copy: " << variable_name << "\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" );
 
    Tag sourceTag;
    MB_CHK_SET_ERR( mb2->tag_get_handle( variable_name.c_str(), sourceTag ), "can't get tag from file" );
 
    int sizeTag = 0;
    MB_CHK_SET_ERR( mb2->tag_get_length( sourceTag, sizeTag ), "can't get size of tag " );
 
    DataType type;
    MB_CHK_SET_ERR( mb2->tag_get_data_type( sourceTag, type ), "can't get type of tag " );
 
    int sizeInBytes = 0;
    MB_CHK_SET_ERR( mb2->tag_get_bytes( sourceTag, sizeInBytes ), "can't get size in bytes of tag " );
 
    Tag newTag;
    /*
     *  ErrorCode tag_get_handle( const char* name,
                                      int size,
                                      DataType type,
                                      Tag& tag_handle,
                                      unsigned flags = 0,
                                      const void* default_value = 0 )
     */
    void* defVal;
    int defInt       = -100000;
    double defDouble = -1.e10;
    if( type == MB_TYPE_INTEGER )
    {
        defVal = (void*)( &defInt );
    }
    else if( type == MB_TYPE_DOUBLE )
    {
        defVal = (void*)( &defDouble );
    }
 
    MB_CHK_SET_ERR( mb->tag_get_handle( variable_name.c_str(), sizeTag, type, newTag, MB_TAG_DENSE | MB_TAG_CREAT,
                                        defVal ),
                    "can't create new tag " );
 
    // 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 " );
    if( 0 != dual_mesh )
    {
        // verts will be polygons
        MB_CHK_SET_ERR( mb->get_entities_by_dimension( 0, 2, iniVerts ), "can't get polygons 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
 
    char* valTag = new char[sizeInBytes];
 
    std::cout << " size of tag in bytes:" << sizeInBytes << "\n";
    Range sourceVerts;
    MB_CHK_SET_ERR( mb2->get_entities_by_dimension( 0, 0, sourceVerts ), "can't get verts on source mesh " );
    for( Range::iterator sit = sourceVerts.begin(); sit != sourceVerts.end(); sit++ )
    {
        int globalId              = 0;
        EntityHandle sourceHandle = *sit;
        MB_CHK_SET_ERR( mb2->tag_get_data( gid2, &sourceHandle, 1, &globalId ), "can't get id on source mesh " );
        // iniVert could be a polygon, actually
        EntityHandle iniVert = fromGidToEh[globalId];
        // find the value of source tag
        MB_CHK_SET_ERR( mb2->tag_get_data( sourceTag, &sourceHandle, 1, (void*)valTag ),
                        "can't get value on source tag " );
 
        MB_CHK_SET_ERR( mb->tag_set_data( newTag, &iniVert, 1, (void*)valTag ),
                        "can't set value on initial mesh, new tag " );
    }
 
    // save file
    MB_CHK_SET_ERR( mb->write_file( outfile.c_str() ), "can't write file" );
 
    delete[] valTag;
    delete mb;
    delete mb2;
 
    return 0;
}

References ProgOptions::addOpt(), moab::Range::begin(), moab::Range::end(), ErrorCode, moab::Core::get_entities_by_dimension(), moab::Core::load_file(), mb, MB_CHK_SET_ERR, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, MB_TYPE_INTEGER, ProgOptions::parseCommandLine(), ProgOptions::printHelp(), moab::Range::size(), moab::Core::tag_get_bytes(), moab::Core::tag_get_data(), moab::Core::tag_get_data_type(), moab::Core::tag_get_handle(), moab::Core::tag_get_length(), moab::Core::tag_set_data(), and moab::Core::write_file().