addPCdata.cpp

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/** @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;
}