ReadNC.cpp

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#include "ReadNC.hpp"
#include "NCHelper.hpp"
 
#include "moab/ReadUtilIface.hpp"
#include "MBTagConventions.hpp"
#include "moab/FileOptions.hpp"
 
namespace moab
{
 
ReaderIface* ReadNC::factory( Interface* iface )
{
 return new ReadNC( iface );
}
 
ReadNC::ReadNC( Interface* impl )
 : mbImpl( impl ), fileId( -1 ), mGlobalIdTag( 0 ), mpFileIdTag( NULL ), dbgOut( stderr ), isParallel( false ),
 partMethod( ScdParData::ALLJORKORI ), scdi( NULL ),
#ifdef MOAB_HAVE_MPI
 myPcomm( NULL ),
#endif
 noMesh( false ), noVars( false ), spectralMesh( false ), noMixedElements( false ), noEdges( false ),
 gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ), myHelper( NULL )
{
 assert( impl != NULL );
 impl->query_interface( readMeshIface );
}
 
ReadNC::~ReadNC()
{
 mbImpl->release_interface( readMeshIface );
 if( myHelper != NULL ) delete myHelper;
}
 
ErrorCode ReadNC::load_file( const char* file_name,
 const EntityHandle* file_set,
 const FileOptions& opts,
 const ReaderIface::SubsetList* /*subset_list*/,
 const Tag* file_id_tag )
{
 // See if opts has variable(s) specified
 std::vector< std::string > var_names;
 std::vector< int > tstep_nums;
 std::vector< double > tstep_vals;
 
 // Get and cache predefined tag handles
 mGlobalIdTag = mbImpl->globalId_tag();
 // Store the pointer to the tag; if not null, set when global id tag
 // is set too, with the same data, duplicated
 mpFileIdTag = file_id_tag;
 
 ErrorCode rval = parse_options( opts, var_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );
 
 // Open the file
 dbgOut.tprintf( 1, "Opening file %s\n", file_name );
 fileName = std::string( file_name );
 int success;
 
#ifdef MOAB_HAVE_PNETCDF
 if( isParallel )
 success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, 0, MPI_INFO_NULL, &fileId );
 else
 success = NCFUNC( open )( MPI_COMM_SELF, file_name, 0, MPI_INFO_NULL, &fileId );
#else
 success = NCFUNC( open )( file_name, 0, &fileId );
#endif
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name );
 
 // Read the header (num dimensions, dimensions, num variables, global attribs)
 rval = read_header();MB_CHK_SET_ERR( rval, "Trouble reading file header" );
 
 // Make sure there's a file set to put things in
 EntityHandle tmp_set;
 if( noMesh && !file_set )
 {
 MB_SET_ERR( MB_FAILURE, "NOMESH option requires non-NULL file set on input" );
 }
 else if( !file_set || ( file_set && *file_set == 0 ) )
 {
 rval = mbImpl->create_meshset( MESHSET_SET, tmp_set );MB_CHK_SET_ERR( rval, "Trouble creating file set" );
 }
 else
 tmp_set = *file_set;
 
 // Get the scd interface
 scdi = NULL;
 rval = mbImpl->query_interface( scdi );
 if( NULL == scdi ) return MB_FAILURE;
 
 if( NULL != myHelper ) delete myHelper;
 
 // Get appropriate NC helper instance based on information read from the header
 myHelper = NCHelper::get_nc_helper( this, fileId, opts, tmp_set );
 if( NULL == myHelper )
 {
 MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
 }
 
 // Initialize mesh values
 rval = myHelper->init_mesh_vals();MB_CHK_SET_ERR( rval, "Trouble initializing mesh values" );
 
 // Check existing mesh from last read
 if( noMesh && !noVars )
 {
 rval = myHelper->check_existing_mesh();MB_CHK_SET_ERR( rval, "Trouble checking mesh from last read" );
 }
 
 // Create some conventional tags, e.g. __NUM_DIMS
 // For multiple reads to a specified file set, we assume a single file, or a series of
 // files with separated timesteps. Keep a flag on the file set to prevent conventional
 // tags from being created again on a second read
 Tag convTagsCreated = 0;
 int def_val = 0;
 rval = mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
 MB_TAG_SPARSE | MB_TAG_CREAT, &def_val );MB_CHK_SET_ERR( rval, "Trouble getting _CONV_TAGS_CREATED tag" );
 int create_conv_tags_flag = 0;
 rval = mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );
 // The first read to the file set
 if( 0 == create_conv_tags_flag )
 {
 // Read dimensions (coordinate variables) by default to create tags like __<var_name>_DIMS
 // This is done only once (assume that all files read to the file set have the same
 // dimensions)
 rval = myHelper->read_variables( dimNames, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading dimensions" );
 
 rval = myHelper->create_conventional_tags( tstep_nums );MB_CHK_SET_ERR( rval, "Trouble creating NC conventional tags" );
 
 create_conv_tags_flag = 1;
 rval = mbImpl->tag_set_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );MB_CHK_SET_ERR( rval, "Trouble setting data to _CONV_TAGS_CREATED tag" );
 }
 // Another read to the file set
 else
 {
 if( tStepBase > -1 )
 {
 // If timesteps spread across files, merge time values read
 // from current file to existing time tag
 rval = myHelper->update_time_tag_vals();MB_CHK_SET_ERR( rval, "Trouble updating time tag values" );
 }
 }
 
 // Create mesh vertex/edge/face sequences
 Range faces;
 if( !noMesh )
 {
 rval = myHelper->create_mesh( faces );MB_CHK_SET_ERR( rval, "Trouble creating mesh" );
 }
 
 // Read specified variables onto grid
 if( !noVars )
 {
 if( var_names.empty() )
 {
 // If VARIABLE option is missing, read all variables
 rval = myHelper->read_variables( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading all variables" );
 }
 else
 {
 // Exclude dimensions that are read to the file set by default
 std::vector< std::string > non_dim_var_names;
 for( unsigned int i = 0; i < var_names.size(); i++ )
 {
 if( std::find( dimNames.begin(), dimNames.end(), var_names[i] ) == dimNames.end() )
 non_dim_var_names.push_back( var_names[i] );
 }
 
 if( !non_dim_var_names.empty() )
 {
 rval = myHelper->read_variables( non_dim_var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading specified variables" );
 }
 }
 }
 
#ifdef MOAB_HAVE_MPI
 // Create partition set, and populate with elements
 if( isParallel )
 {
 // Write partition tag name on partition set
 Tag part_tag = myPcomm->partition_tag();
 int dum_rank = myPcomm->proc_config().proc_rank();
 // the tmp_set is the file_set
 rval = mbImpl->tag_set_data( part_tag, &tmp_set, 1, &dum_rank );MB_CHK_SET_ERR( rval, "Trouble writing partition tag name on partition set" );
 }
#endif
 
 mbImpl->release_interface( scdi );
 scdi = NULL;
 
 // Close the file
 success = NCFUNC( close )( fileId );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::parse_options( const FileOptions& opts,
 std::vector< std::string >& var_names,
 std::vector< int >& tstep_nums,
 std::vector< double >& tstep_vals )
{
 int tmpval;
 if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
 {
 dbgOut.set_verbosity( tmpval );
 dbgOut.set_prefix( "NC " );
 }
 
 ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
 if( MB_TYPE_OUT_OF_RANGE == rval )
 noVars = true;
 else
 noVars = false;
 
 opts.get_ints_option( "TIMESTEP", tstep_nums );
 opts.get_reals_option( "TIMEVAL", tstep_vals );
 
 rval = opts.get_null_option( "NOMESH" );
 if( MB_SUCCESS == rval ) noMesh = true;
 
 rval = opts.get_null_option( "SPECTRAL_MESH" );
 if( MB_SUCCESS == rval ) spectralMesh = true;
 
 rval = opts.get_null_option( "NO_MIXED_ELEMENTS" );
 if( MB_SUCCESS == rval ) noMixedElements = true;
 
 rval = opts.get_null_option( "NO_EDGES" );
 if( MB_SUCCESS == rval ) noEdges = true;
 
 if( 2 <= dbgOut.get_verbosity() )
 {
 if( !var_names.empty() )
 {
 std::cerr << "Variables requested: ";
 for( unsigned int i = 0; i < var_names.size(); i++ )
 std::cerr << var_names[i];
 std::cerr << std::endl;
 }
 
 if( !tstep_nums.empty() )
 {
 std::cerr << "Timesteps requested: ";
 for( unsigned int i = 0; i < tstep_nums.size(); i++ )
 std::cerr << tstep_nums[i];
 std::cerr << std::endl;
 }
 
 if( !tstep_vals.empty() )
 {
 std::cerr << "Time vals requested: ";
 for( unsigned int i = 0; i < tstep_vals.size(); i++ )
 std::cerr << tstep_vals[i];
 std::cerr << std::endl;
 }
 }
 
 rval = opts.get_int_option( "GATHER_SET", 0, gatherSetRank );
 if( MB_TYPE_OUT_OF_RANGE == rval )
 {
 MB_SET_ERR( rval, "Invalid value for GATHER_SET option" );
 }
 
 rval = opts.get_int_option( "TIMESTEPBASE", 0, tStepBase );
 if( MB_TYPE_OUT_OF_RANGE == rval )
 {
 MB_SET_ERR( rval, "Invalid value for TIMESTEPBASE option" );
 }
 
 rval = opts.get_int_option( "TRIVIAL_PARTITION_SHIFT", 1, trivialPartitionShift );
 if( MB_TYPE_OUT_OF_RANGE == rval )
 {
 MB_SET_ERR( rval, "Invalid value for TRIVIAL_PARTITION_SHIFT option" );
 }
 
#ifdef MOAB_HAVE_MPI
 isParallel = ( opts.match_option( "PARALLEL", "READ_PART" ) != MB_ENTITY_NOT_FOUND );
 
 if( !isParallel )
 // Return success here, since rval still has _NOT_FOUND from not finding option
 // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
 // before any use for myPcomm
 return MB_SUCCESS;
 
 int pcomm_no = 0;
 rval = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
 if( MB_TYPE_OUT_OF_RANGE == rval )
 {
 MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
 }
 myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
 if( 0 == myPcomm )
 {
 myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
 }
 const int rank = myPcomm->proc_config().proc_rank();
 dbgOut.set_rank( rank );
 
 int dum;
 rval = opts.match_option( "PARTITION_METHOD", ScdParData::PartitionMethodNames, dum );
 if( MB_FAILURE == rval )
 {
 MB_SET_ERR( rval, "Unknown partition method specified" );
 }
 else if( MB_ENTITY_NOT_FOUND == rval )
 partMethod = ScdParData::ALLJORKORI;
 else
 partMethod = dum;
#endif
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::read_header()
{
 dbgOut.tprint( 1, "Reading header...\n" );
 
 // Get the global attributes
 int numgatts;
 int success;
 success = NCFUNC( inq_natts )( fileId, &numgatts );
 if( success ) MB_SET_ERR( MB_FAILURE, "Couldn't get number of global attributes" );
 
 // Read attributes into globalAtts
 ErrorCode result = get_attributes( NC_GLOBAL, numgatts, globalAtts );MB_CHK_SET_ERR( result, "Trouble getting global attributes" );
 dbgOut.tprintf( 1, "Read %u attributes\n", (unsigned int)globalAtts.size() );
 
 // Read in dimensions into dimNames and dimLens
 result = get_dimensions( fileId, dimNames, dimLens );MB_CHK_SET_ERR( result, "Trouble getting dimensions" );
 dbgOut.tprintf( 1, "Read %u dimensions\n", (unsigned int)dimNames.size() );
 
 // Read in variables into varInfo
 result = get_variables();MB_CHK_SET_ERR( result, "Trouble getting variables" );
 dbgOut.tprintf( 1, "Read %u variables\n", (unsigned int)varInfo.size() );
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_attributes( int var_id, int num_atts, std::map< std::string, AttData >& atts, const char* prefix )
{
 char dum_name[120];
 
 for( int i = 0; i < num_atts; i++ )
 {
 // Get the name
 int success = NCFUNC( inq_attname )( fileId, var_id, i, dum_name );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting attribute name" );
 
 AttData& data = atts[std::string( dum_name )];
 data.attName = std::string( dum_name );
 success = NCFUNC( inq_att )( fileId, var_id, dum_name, &data.attDataType, &data.attLen );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting info for attribute " << data.attName );
 data.attVarId = var_id;
 
 dbgOut.tprintf( 2, "%sAttribute %s: length=%u, varId=%d, type=%d\n", ( prefix ? prefix : "" ),
 data.attName.c_str(), (unsigned int)data.attLen, data.attVarId, data.attDataType );
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_dimensions( int file_id, std::vector< std::string >& dim_names, std::vector< int >& dim_lens )
{
 // Get the number of dimensions
 int num_dims;
 int success = NCFUNC( inq_ndims )( file_id, &num_dims );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dimensions" );
 
 if( num_dims > NC_MAX_DIMS )
 {
 MB_SET_ERR( MB_FAILURE,
 "ReadNC: File contains " << num_dims << " dims but NetCDF library supports only " << NC_MAX_DIMS );
 }
 
 char dim_name[NC_MAX_NAME + 1];
 NCDF_SIZE dim_len;
 dim_names.resize( num_dims );
 dim_lens.resize( num_dims );
 
 for( int i = 0; i < num_dims; i++ )
 {
 success = NCFUNC( inq_dim )( file_id, i, dim_name, &dim_len );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimension info" );
 
 dim_names[i] = std::string( dim_name );
 dim_lens[i] = dim_len;
 
 dbgOut.tprintf( 2, "Dimension %s, length=%u\n", dim_name, (unsigned int)dim_len );
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::get_variables()
{
 // First cache the number of time steps
 std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), "time" );
 if( vit == dimNames.end() ) vit = std::find( dimNames.begin(), dimNames.end(), "t" );
 
 int ntimes = 0;
 if( vit != dimNames.end() ) ntimes = dimLens[vit - dimNames.begin()];
 if( !ntimes ) ntimes = 1;
 
 // Get the number of variables
 int num_vars;
 int success = NCFUNC( inq_nvars )( fileId, &num_vars );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of variables" );
 
 if( num_vars > NC_MAX_VARS )
 {
 MB_SET_ERR( MB_FAILURE,
 "ReadNC: File contains " << num_vars << " vars but NetCDF library supports only " << NC_MAX_VARS );
 }
 
 char var_name[NC_MAX_NAME + 1];
 int var_ndims;
 
 for( int i = 0; i < num_vars; i++ )
 {
 // Get the name first, so we can allocate a map iterate for this var
 success = NCFUNC( inq_varname )( fileId, i, var_name );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting variable name" );
 VarData& data = varInfo[std::string( var_name )];
 data.varName = std::string( var_name );
 data.varId = i;
 data.varTags.resize( ntimes, 0 );
 
 // Get the data type
 success = NCFUNC( inq_vartype )( fileId, i, &data.varDataType );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting data type for variable " << data.varName );
 
 // Get the number of dimensions, then the dimensions
 success = NCFUNC( inq_varndims )( fileId, i, &var_ndims );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
 data.varDims.resize( var_ndims );
 
 success = NCFUNC( inq_vardimid )( fileId, i, &data.varDims[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimensions for variable " << data.varName );
 
 // Finally, get the number of attributes, then the attributes
 success = NCFUNC( inq_varnatts )( fileId, i, &data.numAtts );
 if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
 
 // Print debug info here so attribute info comes afterwards
 dbgOut.tprintf( 2, "Variable %s: Id=%d, numAtts=%d, datatype=%d, num_dims=%u\n", data.varName.c_str(),
 data.varId, data.numAtts, data.varDataType, (unsigned int)data.varDims.size() );
 
 ErrorCode rval = get_attributes( i, data.numAtts, data.varAtts, " " );MB_CHK_SET_ERR( rval, "Trouble getting attributes for variable " << data.varName );
 }
 
 return MB_SUCCESS;
}
 
ErrorCode ReadNC::read_tag_values( const char*,
 const char*,
 const FileOptions&,
 std::vector< int >&,
 const SubsetList* )
{
 return MB_FAILURE;
}
 
} // namespace moab