VisTags.cpp

tool for visualizing multi level tags
To run: VisTags <inp_file> <outfile> -O <read_opts> -t <tags> -l <levels> -d <dim>

In this example, it is shown how to create some simple tags for those tags that come from climate data, multiple levels. you can read directly nc data, or *.h5m file that will have the tag with multi levels output will be a vtk file with dense tags of form tag_name_<level> the tag name might contain a time index too, like T0 or U0 <tag> is a list of tags, separated by commas, no spaces <levels> is a list of levels, separated by commas, no spaces dimension of entities with the tags will be specified with -d (default 2)

an example of use

VisTags gcrm_r3.nc out.vtk -O VARIABLE=u -t u0,u1 -l 0,1,2 -d 2 (we knew that it had variable u in the file, that it had 256 levels, that there are 2 time steps, etc)

or VisTags gcrm_r3.nc out.vtk -t u0 -l 0,1,2 -d 2 (it will read all variables, but we need to know that u0 will be created as a tag)

the out.vtk file will contain u0_0, u0_1, as simple dense double tags

/** @example VisTags.cpp \n
 * \brief tool for visualizing multi level tags \n
 * <b>To run</b>: VisTags <inp_file> <outfile> -O <read_opts> -t <tags> -l <levels> -d <dim> \n
 *
 * In this example, it is shown how to create some simple tags for those tags that come from
 * climate data, multiple levels.
 * you can read directly nc data, or *.h5m file that will have the tag with multi levels
 * output will be a vtk file with dense tags of form tag_name_<level>
 * the tag name might contain a time index too, like T0 or U0
 * <tag> is a list of tags, separated by commas, no spaces
 * <levels> is a list of levels, separated by commas, no spaces
 * dimension of entities with the tags will be specified with -d (default 2)
 *
 * an example of use
 *
 * VisTags gcrm_r3.nc out.vtk -O VARIABLE=u -t u0,u1 -l 0,1,2 -d 2
 * (we knew that it had variable u in the file, that it had 256 levels, that there are 2 time
 * steps, etc)
 *
 * or
 * VisTags gcrm_r3.nc out.vtk -t u0 -l 0,1,2 -d 2
 * (it will read all variables, but we need to know that u0 will be created as a tag)
 *
 * the out.vtk file will contain u0_0, u0_1, as simple dense double tags
 */
 
#include <iostream>
#include <vector>
#include <sstream>
#include <string>
 
// Include header for MOAB instance and tag conventions
#include "moab/Core.hpp"
#include "MBTagConventions.hpp"
#include "moab/FileOptions.hpp"
#ifdef MOAB_HAVE_MPI
#include "moab/ParallelComm.hpp"
#endif
using namespace moab;
using namespace std;
 
int main( int argc, char** argv )
{
#ifdef MOAB_HAVE_NETCDF
 
#ifdef MOAB_HAVE_MPI
 MPI_Init( &argc, &argv );
#endif
 
 ErrorCode rval;
 string file_input, file_output;
 string read_opts, tags; // Tags to write, separated by commas; it is the name of the tag
 if( argc < 2 )
 {
 file_input = string( MESH_DIR ) + string( "/io/gcrm_r3.nc" );
 file_output = "VisTagsOut.vtk";
 }
 else
 {
 file_input = argv[1];
 file_output = argv[2];
 }
 read_opts = "";
 tags = "";
 
 // Instantiate
 Interface* mb = new( std::nothrow ) Core;
 if( NULL == mb ) return 1;
 
 int dimension = 2;
 // In MOAB, it may have index after reading (T0, T1, etc)
 char* levels = NULL; // Levels, separated by commas, no spaces (like 0, 1, 19)
 if( argc > 3 )
 {
 int index = 3;
 while( index < argc )
 {
 if( !strcmp( argv[index], "-O" ) ) // This is for reading options, optional
 read_opts = argv[++index];
 if( !strcmp( argv[index], "-t" ) ) tags = argv[++index];
 if( !strcmp( argv[index], "-l" ) ) levels = argv[++index];
 if( !strcmp( argv[index], "-d" ) ) dimension = atoi( argv[++index] );
 index++;
 }
 }
 
 ostringstream opts;
 opts << ";;TAGS=" << tags << ";LEVELS=" << levels << "\0";
 FileOptions fo( opts.str().c_str() );
 
 vector< string > tagsNames;
 vector< int > levelsArray;
 fo.get_strs_option( "TAGS", tagsNames );
 fo.get_ints_option( "LEVELS", levelsArray );
 
 // Load the input file with the specified options
 rval = mb->load_file( file_input.c_str(), 0, read_opts.c_str() );MB_CHK_SET_ERR( rval, "not loading file" );
 
 Range ents;
 rval = mb->get_entities_by_dimension( 0, dimension, ents );MB_CHK_SET_ERR( rval, "not getting ents" );
 
 // Now create double tags for entities of dimension
 for( size_t i = 0; i < tagsNames.size(); i++ )
 {
 string tagName = tagsNames[i];
 Tag tagh;
 rval = mb->tag_get_handle( tagName.c_str(), tagh );
 if( MB_SUCCESS != rval )
 {
 cout << "not getting tag " << tagName.c_str() << "\n";
 continue;
 }
 
 int len = 0;
 rval = mb->tag_get_length( tagh, len );
 if( MB_SUCCESS != rval )
 {
 cout << "not getting tag len " << tagName.c_str() << "\n";
 continue;
 }
 
 DataType type;
 rval = mb->tag_get_data_type( tagh, type );
 if( MB_SUCCESS != rval )
 {
 cout << "not getting tag type " << tagName.c_str() << "\n";
 continue;
 }
 
 int count;
 void* dataptr; // Assume double tags, for simplicity
 rval = mb->tag_iterate( tagh, ents.begin(), ents.end(), count, dataptr );
 if( MB_SUCCESS != rval || count != (int)ents.size() )
 {
 cout << "not getting tag iterate right " << tagName.c_str() << "\n";
 continue;
 }
 
 // Now create a new tag, with a new name, concatenated, and copy data there , for each level
 for( size_t j = 0; j < levelsArray.size(); j++ )
 {
 int level = levelsArray[j];
 if( level >= len )
 {
 cout << "level too big at " << level << "\n";
 continue;
 }
 
 ostringstream newTagName;
 newTagName << tagName << "_" << level;
 Tag newTagh;
 rval = mb->tag_get_handle( newTagName.str().c_str(), 1, type, newTagh, MB_TAG_DENSE | MB_TAG_CREAT );
 if( MB_SUCCESS != rval )
 {
 cout << "not getting new tag " << newTagName.str() << "\n";
 continue;
 }
 
 void* newDataPtr;
 rval = mb->tag_iterate( newTagh, ents.begin(), ents.end(), count, newDataPtr );
 if( MB_SUCCESS != rval || count != (int)ents.size() )
 {
 cout << "not getting new tag iterate " << newTagName.str() << "\n";
 continue;
 }
 
 if( MB_TYPE_DOUBLE == type )
 {
 double* ptrD = (double*)newDataPtr;
 double* oldData = (double*)dataptr;
 for( int k = 0; k < count; k++, ptrD++ )
 *ptrD = oldData[level + count * k];
 }
 } // for (size_t j = 0; j < levelsArray.size(); j++)
 
 mb->tag_delete( tagh ); // No need for the tag anymore, write it to the new file
 } // for (size_t i = 0; i < tagsNames.size(); i++)
 
 rval = mb->write_file( file_output.c_str() );MB_CHK_SET_ERR( rval, "Can't write file " << file_output );
 cout << "Successfully wrote file " << file_output << "\n";
 
 delete mb;
 
#ifdef MOAB_HAVE_MPI
 MPI_Finalize();
#endif
#else
 std::cout << " configure with netcdf for this example to work\n";
#endif
 return 0;
}