Mesh Oriented datABase  (version 5.4.1)
Array-based unstructured mesh datastructure
ReadNC.cpp
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00001 #include "ReadNC.hpp"
00002 #include "NCHelper.hpp"
00003 
00004 #include "moab/ReadUtilIface.hpp"
00005 #include "MBTagConventions.hpp"
00006 #include "moab/FileOptions.hpp"
00007 
00008 namespace moab
00009 {
00010 
00011 ReaderIface* ReadNC::factory( Interface* iface )
00012 {
00013     return new ReadNC( iface );
00014 }
00015 
00016 ReadNC::ReadNC( Interface* impl )
00017     : mbImpl( impl ), fileId( -1 ), mGlobalIdTag( 0 ), mpFileIdTag( NULL ), dbgOut( stderr ), isParallel( false ),
00018       partMethod( ScdParData::ALLJORKORI ), scdi( NULL ),
00019 #ifdef MOAB_HAVE_MPI
00020       myPcomm( NULL ),
00021 #endif
00022       noMesh( false ), noVars( false ), spectralMesh( false ), noMixedElements( false ), noEdges( false ),
00023       gatherSetRank( -1 ), tStepBase( -1 ), trivialPartitionShift( 0 ), myHelper( NULL )
00024 {
00025     assert( impl != NULL );
00026     impl->query_interface( readMeshIface );
00027 }
00028 
00029 ReadNC::~ReadNC()
00030 {
00031     mbImpl->release_interface( readMeshIface );
00032     if( myHelper != NULL ) delete myHelper;
00033 }
00034 
00035 ErrorCode ReadNC::load_file( const char* file_name,
00036                              const EntityHandle* file_set,
00037                              const FileOptions& opts,
00038                              const ReaderIface::SubsetList* /*subset_list*/,
00039                              const Tag* file_id_tag )
00040 {
00041     // See if opts has variable(s) specified
00042     std::vector< std::string > var_names;
00043     std::vector< int > tstep_nums;
00044     std::vector< double > tstep_vals;
00045 
00046     // Get and cache predefined tag handles
00047     mGlobalIdTag = mbImpl->globalId_tag();
00048     // Store the pointer to the tag; if not null, set when global id tag
00049     // is set too, with the same data, duplicated
00050     mpFileIdTag = file_id_tag;
00051 
00052     ErrorCode rval = parse_options( opts, var_names, tstep_nums, tstep_vals );MB_CHK_SET_ERR( rval, "Trouble parsing option string" );
00053 
00054     // Open the file
00055     dbgOut.tprintf( 1, "Opening file %s\n", file_name );
00056     fileName = std::string( file_name );
00057     int success;
00058 
00059 #ifdef MOAB_HAVE_PNETCDF
00060     if( isParallel )
00061         success = NCFUNC( open )( myPcomm->proc_config().proc_comm(), file_name, 0, MPI_INFO_NULL, &fileId );
00062     else
00063         success = NCFUNC( open )( MPI_COMM_SELF, file_name, 0, MPI_INFO_NULL, &fileId );
00064 #else
00065     success = NCFUNC( open )( file_name, 0, &fileId );
00066 #endif
00067     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble opening file " << file_name );
00068 
00069     // Read the header (num dimensions, dimensions, num variables, global attribs)
00070     rval = read_header();MB_CHK_SET_ERR( rval, "Trouble reading file header" );
00071 
00072     // Make sure there's a file set to put things in
00073     EntityHandle tmp_set;
00074     if( noMesh && !file_set )
00075     {
00076         MB_SET_ERR( MB_FAILURE, "NOMESH option requires non-NULL file set on input" );
00077     }
00078     else if( !file_set || ( file_set && *file_set == 0 ) )
00079     {
00080         rval = mbImpl->create_meshset( MESHSET_SET, tmp_set );MB_CHK_SET_ERR( rval, "Trouble creating file set" );
00081     }
00082     else
00083         tmp_set = *file_set;
00084 
00085     // Get the scd interface
00086     scdi = NULL;
00087     rval = mbImpl->query_interface( scdi );
00088     if( NULL == scdi ) return MB_FAILURE;
00089 
00090     if( NULL != myHelper ) delete myHelper;
00091 
00092     // Get appropriate NC helper instance based on information read from the header
00093     myHelper = NCHelper::get_nc_helper( this, fileId, opts, tmp_set );
00094     if( NULL == myHelper )
00095     {
00096         MB_SET_ERR( MB_FAILURE, "Failed to get NCHelper class instance" );
00097     }
00098 
00099     // Initialize mesh values
00100     rval = myHelper->init_mesh_vals();MB_CHK_SET_ERR( rval, "Trouble initializing mesh values" );
00101 
00102     // Check existing mesh from last read
00103     if( noMesh && !noVars )
00104     {
00105         rval = myHelper->check_existing_mesh();MB_CHK_SET_ERR( rval, "Trouble checking mesh from last read" );
00106     }
00107 
00108     // Create some conventional tags, e.g. __NUM_DIMS
00109     // For multiple reads to a specified file set, we assume a single file, or a series of
00110     // files with separated timesteps. Keep a flag on the file set to prevent conventional
00111     // tags from being created again on a second read
00112     Tag convTagsCreated = 0;
00113     int def_val         = 0;
00114     rval                = mbImpl->tag_get_handle( "__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated,
00115                                                   MB_TAG_SPARSE | MB_TAG_CREAT, &def_val );MB_CHK_SET_ERR( rval, "Trouble getting _CONV_TAGS_CREATED tag" );
00116     int create_conv_tags_flag = 0;
00117     rval                      = mbImpl->tag_get_data( convTagsCreated, &tmp_set, 1, &create_conv_tags_flag );
00118     // The first read to the file set
00119     if( 0 == create_conv_tags_flag )
00120     {
00121         // Read dimensions (coordinate variables) by default to create tags like __<var_name>_DIMS
00122         // This is done only once (assume that all files read to the file set have the same
00123         // dimensions)
00124         rval = myHelper->read_variables( dimNames, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading dimensions" );
00125 
00126         rval = myHelper->create_conventional_tags( tstep_nums );MB_CHK_SET_ERR( rval, "Trouble creating NC conventional tags" );
00127 
00128         create_conv_tags_flag = 1;
00129         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" );
00130     }
00131     // Another read to the file set
00132     else
00133     {
00134         if( tStepBase > -1 )
00135         {
00136             // If timesteps spread across files, merge time values read
00137             // from current file to existing time tag
00138             rval = myHelper->update_time_tag_vals();MB_CHK_SET_ERR( rval, "Trouble updating time tag values" );
00139         }
00140     }
00141 
00142     // Create mesh vertex/edge/face sequences
00143     Range faces;
00144     if( !noMesh )
00145     {
00146         rval = myHelper->create_mesh( faces );MB_CHK_SET_ERR( rval, "Trouble creating mesh" );
00147     }
00148 
00149     // Read specified variables onto grid
00150     if( !noVars )
00151     {
00152         if( var_names.empty() )
00153         {
00154             // If VARIABLE option is missing, read all variables
00155             rval = myHelper->read_variables( var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading all variables" );
00156         }
00157         else
00158         {
00159             // Exclude dimensions that are read to the file set by default
00160             std::vector< std::string > non_dim_var_names;
00161             for( unsigned int i = 0; i < var_names.size(); i++ )
00162             {
00163                 if( std::find( dimNames.begin(), dimNames.end(), var_names[i] ) == dimNames.end() )
00164                     non_dim_var_names.push_back( var_names[i] );
00165             }
00166 
00167             if( !non_dim_var_names.empty() )
00168             {
00169                 rval = myHelper->read_variables( non_dim_var_names, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble reading specified variables" );
00170             }
00171         }
00172     }
00173 
00174 #ifdef MOAB_HAVE_MPI
00175     // Create partition set, and populate with elements
00176     if( isParallel )
00177     {
00178         // Write partition tag name on partition set
00179         Tag part_tag = myPcomm->partition_tag();
00180         int dum_rank = myPcomm->proc_config().proc_rank();
00181         // the tmp_set is the file_set
00182         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" );
00183     }
00184 #endif
00185 
00186     mbImpl->release_interface( scdi );
00187     scdi = NULL;
00188 
00189     // Close the file
00190     success = NCFUNC( close )( fileId );
00191     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble closing file" );
00192 
00193     return MB_SUCCESS;
00194 }
00195 
00196 ErrorCode ReadNC::parse_options( const FileOptions& opts,
00197                                  std::vector< std::string >& var_names,
00198                                  std::vector< int >& tstep_nums,
00199                                  std::vector< double >& tstep_vals )
00200 {
00201     int tmpval;
00202     if( MB_SUCCESS == opts.get_int_option( "DEBUG_IO", 1, tmpval ) )
00203     {
00204         dbgOut.set_verbosity( tmpval );
00205         dbgOut.set_prefix( "NC " );
00206     }
00207 
00208     ErrorCode rval = opts.get_strs_option( "VARIABLE", var_names );
00209     if( MB_TYPE_OUT_OF_RANGE == rval )
00210         noVars = true;
00211     else
00212         noVars = false;
00213 
00214     opts.get_ints_option( "TIMESTEP", tstep_nums );
00215     opts.get_reals_option( "TIMEVAL", tstep_vals );
00216 
00217     rval = opts.get_null_option( "NOMESH" );
00218     if( MB_SUCCESS == rval ) noMesh = true;
00219 
00220     rval = opts.get_null_option( "SPECTRAL_MESH" );
00221     if( MB_SUCCESS == rval ) spectralMesh = true;
00222 
00223     rval = opts.get_null_option( "NO_MIXED_ELEMENTS" );
00224     if( MB_SUCCESS == rval ) noMixedElements = true;
00225 
00226     rval = opts.get_null_option( "NO_EDGES" );
00227     if( MB_SUCCESS == rval ) noEdges = true;
00228 
00229     if( 2 <= dbgOut.get_verbosity() )
00230     {
00231         if( !var_names.empty() )
00232         {
00233             std::cerr << "Variables requested: ";
00234             for( unsigned int i = 0; i < var_names.size(); i++ )
00235                 std::cerr << var_names[i];
00236             std::cerr << std::endl;
00237         }
00238 
00239         if( !tstep_nums.empty() )
00240         {
00241             std::cerr << "Timesteps requested: ";
00242             for( unsigned int i = 0; i < tstep_nums.size(); i++ )
00243                 std::cerr << tstep_nums[i];
00244             std::cerr << std::endl;
00245         }
00246 
00247         if( !tstep_vals.empty() )
00248         {
00249             std::cerr << "Time vals requested: ";
00250             for( unsigned int i = 0; i < tstep_vals.size(); i++ )
00251                 std::cerr << tstep_vals[i];
00252             std::cerr << std::endl;
00253         }
00254     }
00255 
00256     rval = opts.get_int_option( "GATHER_SET", 0, gatherSetRank );
00257     if( MB_TYPE_OUT_OF_RANGE == rval )
00258     {
00259         MB_SET_ERR( rval, "Invalid value for GATHER_SET option" );
00260     }
00261 
00262     rval = opts.get_int_option( "TIMESTEPBASE", 0, tStepBase );
00263     if( MB_TYPE_OUT_OF_RANGE == rval )
00264     {
00265         MB_SET_ERR( rval, "Invalid value for TIMESTEPBASE option" );
00266     }
00267 
00268     rval = opts.get_int_option( "TRIVIAL_PARTITION_SHIFT", 1, trivialPartitionShift );
00269     if( MB_TYPE_OUT_OF_RANGE == rval )
00270     {
00271         MB_SET_ERR( rval, "Invalid value for TRIVIAL_PARTITION_SHIFT option" );
00272     }
00273 
00274 #ifdef MOAB_HAVE_MPI
00275     isParallel = ( opts.match_option( "PARALLEL", "READ_PART" ) != MB_ENTITY_NOT_FOUND );
00276 
00277     if( !isParallel )
00278         // Return success here, since rval still has _NOT_FOUND from not finding option
00279         // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel
00280         // before any use for myPcomm
00281         return MB_SUCCESS;
00282 
00283     int pcomm_no = 0;
00284     rval         = opts.get_int_option( "PARALLEL_COMM", pcomm_no );
00285     if( MB_TYPE_OUT_OF_RANGE == rval )
00286     {
00287         MB_SET_ERR( rval, "Invalid value for PARALLEL_COMM option" );
00288     }
00289     myPcomm = ParallelComm::get_pcomm( mbImpl, pcomm_no );
00290     if( 0 == myPcomm )
00291     {
00292         myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
00293     }
00294     const int rank = myPcomm->proc_config().proc_rank();
00295     dbgOut.set_rank( rank );
00296 
00297     int dum;
00298     rval = opts.match_option( "PARTITION_METHOD", ScdParData::PartitionMethodNames, dum );
00299     if( MB_FAILURE == rval )
00300     {
00301         MB_SET_ERR( rval, "Unknown partition method specified" );
00302     }
00303     else if( MB_ENTITY_NOT_FOUND == rval )
00304         partMethod = ScdParData::ALLJORKORI;
00305     else
00306         partMethod = dum;
00307 #endif
00308 
00309     return MB_SUCCESS;
00310 }
00311 
00312 ErrorCode ReadNC::read_header()
00313 {
00314     dbgOut.tprint( 1, "Reading header...\n" );
00315 
00316     // Get the global attributes
00317     int numgatts;
00318     int success;
00319     success = NCFUNC( inq_natts )( fileId, &numgatts );
00320     if( success ) MB_SET_ERR( MB_FAILURE, "Couldn't get number of global attributes" );
00321 
00322     // Read attributes into globalAtts
00323     ErrorCode result = get_attributes( NC_GLOBAL, numgatts, globalAtts );MB_CHK_SET_ERR( result, "Trouble getting global attributes" );
00324     dbgOut.tprintf( 1, "Read %u attributes\n", (unsigned int)globalAtts.size() );
00325 
00326     // Read in dimensions into dimNames and dimLens
00327     result = get_dimensions( fileId, dimNames, dimLens );MB_CHK_SET_ERR( result, "Trouble getting dimensions" );
00328     dbgOut.tprintf( 1, "Read %u dimensions\n", (unsigned int)dimNames.size() );
00329 
00330     // Read in variables into varInfo
00331     result = get_variables();MB_CHK_SET_ERR( result, "Trouble getting variables" );
00332     dbgOut.tprintf( 1, "Read %u variables\n", (unsigned int)varInfo.size() );
00333 
00334     return MB_SUCCESS;
00335 }
00336 
00337 ErrorCode ReadNC::get_attributes( int var_id, int num_atts, std::map< std::string, AttData >& atts, const char* prefix )
00338 {
00339     char dum_name[120];
00340 
00341     for( int i = 0; i < num_atts; i++ )
00342     {
00343         // Get the name
00344         int success = NCFUNC( inq_attname )( fileId, var_id, i, dum_name );
00345         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting attribute name" );
00346 
00347         AttData& data = atts[std::string( dum_name )];
00348         data.attName  = std::string( dum_name );
00349         success       = NCFUNC( inq_att )( fileId, var_id, dum_name, &data.attDataType, &data.attLen );
00350         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting info for attribute " << data.attName );
00351         data.attVarId = var_id;
00352 
00353         dbgOut.tprintf( 2, "%sAttribute %s: length=%u, varId=%d, type=%d\n", ( prefix ? prefix : "" ),
00354                         data.attName.c_str(), (unsigned int)data.attLen, data.attVarId, data.attDataType );
00355     }
00356 
00357     return MB_SUCCESS;
00358 }
00359 
00360 ErrorCode ReadNC::get_dimensions( int file_id, std::vector< std::string >& dim_names, std::vector< int >& dim_lens )
00361 {
00362     // Get the number of dimensions
00363     int num_dims;
00364     int success = NCFUNC( inq_ndims )( file_id, &num_dims );
00365     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dimensions" );
00366 
00367     if( num_dims > NC_MAX_DIMS )
00368     {
00369         MB_SET_ERR( MB_FAILURE,
00370                     "ReadNC: File contains " << num_dims << " dims but NetCDF library supports only " << NC_MAX_DIMS );
00371     }
00372 
00373     char dim_name[NC_MAX_NAME + 1];
00374     NCDF_SIZE dim_len;
00375     dim_names.resize( num_dims );
00376     dim_lens.resize( num_dims );
00377 
00378     for( int i = 0; i < num_dims; i++ )
00379     {
00380         success = NCFUNC( inq_dim )( file_id, i, dim_name, &dim_len );
00381         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimension info" );
00382 
00383         dim_names[i] = std::string( dim_name );
00384         dim_lens[i]  = dim_len;
00385 
00386         dbgOut.tprintf( 2, "Dimension %s, length=%u\n", dim_name, (unsigned int)dim_len );
00387     }
00388 
00389     return MB_SUCCESS;
00390 }
00391 
00392 ErrorCode ReadNC::get_variables()
00393 {
00394     // First cache the number of time steps
00395     std::vector< std::string >::iterator vit = std::find( dimNames.begin(), dimNames.end(), "time" );
00396     if( vit == dimNames.end() ) vit = std::find( dimNames.begin(), dimNames.end(), "t" );
00397 
00398     int ntimes = 0;
00399     if( vit != dimNames.end() ) ntimes = dimLens[vit - dimNames.begin()];
00400     if( !ntimes ) ntimes = 1;
00401 
00402     // Get the number of variables
00403     int num_vars;
00404     int success = NCFUNC( inq_nvars )( fileId, &num_vars );
00405     if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of variables" );
00406 
00407     if( num_vars > NC_MAX_VARS )
00408     {
00409         MB_SET_ERR( MB_FAILURE,
00410                     "ReadNC: File contains " << num_vars << " vars but NetCDF library supports only " << NC_MAX_VARS );
00411     }
00412 
00413     char var_name[NC_MAX_NAME + 1];
00414     int var_ndims;
00415 
00416     for( int i = 0; i < num_vars; i++ )
00417     {
00418         // Get the name first, so we can allocate a map iterate for this var
00419         success = NCFUNC( inq_varname )( fileId, i, var_name );
00420         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting variable name" );
00421         VarData& data = varInfo[std::string( var_name )];
00422         data.varName  = std::string( var_name );
00423         data.varId    = i;
00424         data.varTags.resize( ntimes, 0 );
00425 
00426         // Get the data type
00427         success = NCFUNC( inq_vartype )( fileId, i, &data.varDataType );
00428         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting data type for variable " << data.varName );
00429 
00430         // Get the number of dimensions, then the dimensions
00431         success = NCFUNC( inq_varndims )( fileId, i, &var_ndims );
00432         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
00433         data.varDims.resize( var_ndims );
00434 
00435         success = NCFUNC( inq_vardimid )( fileId, i, &data.varDims[0] );
00436         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting dimensions for variable " << data.varName );
00437 
00438         // Finally, get the number of attributes, then the attributes
00439         success = NCFUNC( inq_varnatts )( fileId, i, &data.numAtts );
00440         if( success ) MB_SET_ERR( MB_FAILURE, "Trouble getting number of dims for variable " << data.varName );
00441 
00442         // Print debug info here so attribute info comes afterwards
00443         dbgOut.tprintf( 2, "Variable %s: Id=%d, numAtts=%d, datatype=%d, num_dims=%u\n", data.varName.c_str(),
00444                         data.varId, data.numAtts, data.varDataType, (unsigned int)data.varDims.size() );
00445 
00446         ErrorCode rval = get_attributes( i, data.numAtts, data.varAtts, "   " );MB_CHK_SET_ERR( rval, "Trouble getting attributes for variable " << data.varName );
00447     }
00448 
00449     return MB_SUCCESS;
00450 }
00451 
00452 ErrorCode ReadNC::read_tag_values( const char*,
00453                                    const char*,
00454                                    const FileOptions&,
00455                                    std::vector< int >&,
00456                                    const SubsetList* )
00457 {
00458     return MB_FAILURE;
00459 }
00460 
00461 }  // namespace moab
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