addPCdata.cpp

Add point cloud data 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,

/** @example addPCdata.cpp  Add point cloud data
 * 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,
 *
 */
#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
 
#include <cmath>
#include <sstream>
 
using namespace moab;
 
int main( int argc, char* argv[] )
{
 
    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();
 
    rval = mb->load_file( inputfile.c_str() );MB_CHK_SET_ERR( rval, "can't load input file" );
 
    Core* mb2 = new Core();
    rval      = mb2->load_file( sourcefile.c_str() );MB_CHK_SET_ERR( rval, "can't load source file" );
 
    Tag sourceTag;
    rval = mb2->tag_get_handle( variable_name.c_str(), sourceTag );MB_CHK_SET_ERR( rval, "can't get tag from file" );
 
    int sizeTag = 0;
    rval        = mb2->tag_get_length( sourceTag, sizeTag );MB_CHK_SET_ERR( rval, "can't get size of tag " );
 
    DataType type;
    rval = mb2->tag_get_data_type( sourceTag, type );MB_CHK_SET_ERR( rval, "can't get type of tag " );
 
    int sizeInBytes = 0;
    rval            = mb2->tag_get_bytes( sourceTag, sizeInBytes );MB_CHK_SET_ERR( rval, "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 );
    }
 
    rval = mb->tag_get_handle( variable_name.c_str(), sizeTag, type, newTag, MB_TAG_DENSE | MB_TAG_CREAT, defVal );MB_CHK_SET_ERR( rval, "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;
    rval = mb->tag_get_handle( "GLOBAL_ID", gid );MB_CHK_SET_ERR( rval, "can't get GLOBAL_ID tag on ini mesh " );
    rval = mb2->tag_get_handle( "GLOBAL_ID", gid2 );MB_CHK_SET_ERR( rval, "can't get GLOBAL_ID tag on source mesh " );
 
    // get vertices on ini mesh; build
    Range iniVerts;
    rval = mb->get_entities_by_dimension( 0, 0, iniVerts );MB_CHK_SET_ERR( rval, "can't get verts on initial mesh " );
    if( 0 != dual_mesh )
    {
        // verts will be polygons
        rval = mb->get_entities_by_dimension( 0, 2, iniVerts );MB_CHK_SET_ERR( rval, "can't get polygons on initial mesh " );
    }
    std::vector< int > gids;
    gids.resize( iniVerts.size() );
    rval = mb->tag_get_data( gid, iniVerts, &( gids[0] ) );MB_CHK_SET_ERR( rval, "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;
    rval = mb2->get_entities_by_dimension( 0, 0, sourceVerts );MB_CHK_SET_ERR( rval, "can't get verts on source mesh " );
    for( Range::iterator sit = sourceVerts.begin(); sit != sourceVerts.end(); sit++ )
    {
        int globalId              = 0;
        EntityHandle sourceHandle = *sit;
        rval                      = mb2->tag_get_data( gid2, &sourceHandle, 1, &globalId );MB_CHK_SET_ERR( rval, "can't get id on source mesh " );
        // iniVert could be a polygon, actually
        EntityHandle iniVert = fromGidToEh[globalId];
        // find the value of source tag
        rval = mb2->tag_get_data( sourceTag, &sourceHandle, 1, (void*)valTag );MB_CHK_SET_ERR( rval, "can't get value on source tag " );
 
        rval = mb->tag_set_data( newTag, &iniVert, 1, (void*)valTag );MB_CHK_SET_ERR( rval, "can't set value on initial mesh, new tag " );
    }
 
    // save file
    rval = mb->write_file( outfile.c_str() );MB_CHK_SET_ERR( rval, "can't write file" );
 
    delete[] valTag;
    delete mb;
    delete mb2;
 
    return 0;
}