moab::NCHelper Class Reference

Helper class to isolate reading of several different nc file formats. More...

#include <NCHelper.hpp>

Inheritance diagram for moab::NCHelper:

Collaboration diagram for moab::NCHelper:

Classes
class	Node3D

Public Member Functions
	NCHelper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
virtual	~NCHelper ()
virtual ErrorCode	init_mesh_vals ()=0
	Interfaces to be implemented in child classes. More...
virtual ErrorCode	check_existing_mesh ()=0
virtual ErrorCode	create_mesh (Range &faces)=0
virtual ErrorCode	read_variables (std::vector< std::string > &var_names, std::vector< int > &tstep_nums)=0
virtual std::string	get_mesh_type_name ()=0
ErrorCode	create_conventional_tags (const std::vector< int > &tstep_nums)
	Create NC conventional tags. More...
ErrorCode	update_time_tag_vals ()
	Update time tag values if timesteps spread across files. More...

Static Public Member Functions
static ReadNC::NCFormatType	get_nc_format (ReadNC *readNC, int fileId)
	Get appropriate format to read the file. More...
static std::string	get_default_ncformat_options (ReadNC::NCFormatType format)
	Get appropriate format to read the file. More...
static NCHelper *	get_nc_helper (ReadNC *readNC, int fileId, const FileOptions &opts, EntityHandle fileSet)
	Get appropriate helper instance for ReadNC class. More...

Protected Member Functions
ErrorCode	read_variables_setup (std::vector< std::string > &var_names, std::vector< int > &tstep_nums, std::vector< ReadNC::VarData > &vdatas, std::vector< ReadNC::VarData > &vsetdatas)
	Separate set and non-set variables (common to scd mesh and ucd mesh) More...
ErrorCode	read_variables_to_set (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Read set variables (common to scd mesh and ucd mesh) More...
ErrorCode	read_coordinate (const char *var_name, int lmin, int lmax, std::vector< double > &cvals)
ErrorCode	get_tag_to_set (ReadNC::VarData &var_data, int tstep_num, Tag &tagh)
ErrorCode	get_tag_to_nonset (ReadNC::VarData &var_data, int tstep_num, Tag &tagh, int num_lev)
ErrorCode	create_attrib_string (const std::map< std::string, ReadNC::AttData > &attMap, std::string &attString, std::vector< int > &attLen)
	Create a character string attString of attMap. with '\0' terminating each attribute name, ';' separating the data type and value, and ';' separating one name/data type/value from the next'. attLen stores the end position for each name/data type/ value. More...
ErrorCode	create_dummy_variables ()
	For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create a dummy variable with a sparse tag to store the dimension length. More...

Protected Attributes
ReadNC *	_readNC
	Allow NCHelper to directly access members of ReadNC. More...
int	_fileId
	Cache some information from ReadNC. More...
const FileOptions &	_opts
EntityHandle	_fileSet
int	nTimeSteps
	Dimensions of time and level. More...
int	nLevels
std::vector< double >	tVals
	Values for time and level. More...
std::vector< double >	levVals
int	tDim
	Dimension numbers for time and level. More...
int	levDim
std::set< std::string >	ignoredVarNames
	Ignored variables. More...
std::set< std::string >	dummyVarNames
	Dummy variables. More...

Private Member Functions
ErrorCode	read_variables_to_set_allocate (std::vector< ReadNC::VarData > &vdatas, std::vector< int > &tstep_nums)
	Used by read_variables_to_set() More...

Detailed Description

Helper class to isolate reading of several different nc file formats.

Definition at line 24 of file NCHelper.hpp.

Constructor & Destructor Documentation

NCHelper()

moab::NCHelper::NCHelper ( ReadNC *  readNC, int  fileId, const FileOptions &  opts, EntityHandle  fileSet  )

inline

Definition at line 27 of file NCHelper.hpp.

 : _readNC( readNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
 tDim( -1 ), levDim( -1 )
 {
 }

~NCHelper()

virtual moab::NCHelper::~NCHelper ( )

inlinevirtual

Definition at line 32 of file NCHelper.hpp.

{}

Member Function Documentation

check_existing_mesh()

virtual ErrorCode moab::NCHelper::check_existing_mesh ( )

pure virtual

Implemented in moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, moab::NCHelperESMF, and moab::ScdNCHelper.

Referenced by moab::ReadNC::load_file().

create_attrib_string()

ErrorCode moab::NCHelper::create_attrib_string ( const std::map< std::string, ReadNC::AttData > &  attMap, std::string &  attString, std::vector< int > &  attLen  )

protected

Create a character string attString of attMap. with '\0' terminating each attribute name, ';' separating the data type and value, and ';' separating one name/data type/value from the next'. attLen stores the end position for each name/data type/ value.

Definition at line 734 of file NCHelper.cpp.

{
 int success;
 std::stringstream ssAtt;
 unsigned int sz = 0;
 std::map< std::string, ReadNC::AttData >::const_iterator attIt = attMap.begin();
 for( ; attIt != attMap.end(); ++attIt )
 {
 ssAtt << attIt->second.attName;
 ssAtt << '\0';
 void* attData = NULL;
 switch( attIt->second.attDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 sz = attIt->second.attLen;
 attData = (char*)malloc( sz );
 success = NCFUNC( get_att_text )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (char*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read byte/char data for attribute " << attIt->second.attName );
 ssAtt << "char;";
 break;
 case NC_SHORT:
 sz = attIt->second.attLen * sizeof( short );
 attData = (short*)malloc( sz );
 success = NCFUNC( get_att_short )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (short*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read short data for attribute " << attIt->second.attName );
 ssAtt << "short;";
 break;
 case NC_INT:
 sz = attIt->second.attLen * sizeof( int );
 attData = (int*)malloc( sz );
 success = NCFUNC( get_att_int )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (int*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read int data for attribute " << attIt->second.attName );
 ssAtt << "int;";
 break;
 case NC_INT64: // be careful here
 sz = attIt->second.attLen * sizeof( long );
 attData = (long*)malloc( sz );
 success = NCFUNC( get_att_long )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (long*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read int data for attribute " << attIt->second.attName );
 ssAtt << "long;";
 break;
 case NC_FLOAT:
 sz = attIt->second.attLen * sizeof( float );
 attData = (float*)malloc( sz );
 success = NCFUNC( get_att_float )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (float*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read float data for attribute " << attIt->second.attName );
 ssAtt << "float;";
 break;
 case NC_DOUBLE:
 sz = attIt->second.attLen * sizeof( double );
 attData = (double*)malloc( sz );
 success = NCFUNC( get_att_double )( _fileId, attIt->second.attVarId, attIt->second.attName.c_str(),
 (double*)attData );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read double data for attribute " << attIt->second.attName );
 ssAtt << "double;";
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for attribute " << attIt->second.attName );
 }
 char* tmpc = (char*)attData;
 for( unsigned int counter = 0; counter != sz; ++counter )
 ssAtt << tmpc[counter];
 free( attData );
 ssAtt << ';';
 attLen.push_back( ssAtt.str().size() - 1 );
 }
 attVal = ssAtt.str();
 
 return MB_SUCCESS;
}

References _fileId, MB_SET_ERR, MB_SUCCESS, and NCFUNC.

Referenced by create_conventional_tags().

create_conventional_tags()

ErrorCode moab::NCHelper::create_conventional_tags

(

const std::vector< int > &

tstep_nums

)

Create NC conventional tags.

Definition at line 120 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 std::vector< std::string >& dimNames = _readNC->dimNames;
 std::vector< int >& dimLens = _readNC->dimLens;
 std::map< std::string, ReadNC::AttData >& globalAtts = _readNC->globalAtts;
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 DebugOutput& dbgOut = _readNC->dbgOut;
 int& partMethod = _readNC->partMethod;
 ScdInterface* scdi = _readNC->scdi;
 
 ErrorCode rval;
 std::string tag_name;
 
 // <__NUM_DIMS>
 Tag numDimsTag = 0;
 tag_name = "__NUM_DIMS";
 int numDims = dimNames.size();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 1, MB_TYPE_INTEGER, numDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( numDimsTag, &_fileSet, 1, &numDims );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__NUM_VARS>
 Tag numVarsTag = 0;
 tag_name = "__NUM_VARS";
 int numVars = varInfo.size();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 1, MB_TYPE_INTEGER, numVarsTag, MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( numVarsTag, &_fileSet, 1, &numVars );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__DIM_NAMES>
 Tag dimNamesTag = 0;
 tag_name = "__DIM_NAMES";
 std::string dimnames;
 unsigned int dimNamesSz = dimNames.size();
 for( unsigned int i = 0; i != dimNamesSz; i++ )
 {
 dimnames.append( dimNames[i] );
 dimnames.push_back( '\0' );
 }
 int dimnamesSz = dimnames.size();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 const void* ptr = dimnames.c_str();
 rval = mbImpl->tag_set_by_ptr( dimNamesTag, &_fileSet, 1, &ptr, &dimnamesSz );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__DIM_LENS>
 Tag dimLensTag = 0;
 tag_name = "__DIM_LENS";
 int dimLensSz = dimLens.size();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 ptr = &( dimLens[0] );
 rval = mbImpl->tag_set_by_ptr( dimLensTag, &_fileSet, 1, &ptr, &dimLensSz );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__VAR_NAMES>
 Tag varNamesTag = 0;
 tag_name = "__VAR_NAMES";
 std::string varnames;
 std::map< std::string, ReadNC::VarData >::iterator mapIter;
 for( mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter )
 {
 varnames.append( mapIter->first );
 varnames.push_back( '\0' );
 }
 int varnamesSz = varnames.size();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 ptr = varnames.c_str();
 rval = mbImpl->tag_set_by_ptr( varNamesTag, &_fileSet, 1, &ptr, &varnamesSz );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // __<dim_name>_LOC_MINMAX (for time)
 for( unsigned int i = 0; i != dimNamesSz; i++ )
 {
 if( dimNames[i] == "time" || dimNames[i] == "Time" || dimNames[i] == "t" )
 {
 // some files might have Time dimension as 0, it will not appear in any
 // variables, so skip it
 if( nTimeSteps == 0 ) continue;
 std::stringstream ss_tag_name;
 ss_tag_name << "__" << dimNames[i] << "_LOC_MINMAX";
 tag_name = ss_tag_name.str();
 Tag tagh = 0;
 std::vector< int > val( 2, 0 );
 val[0] = 0;
 val[1] = nTimeSteps - 1;
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( tagh, &_fileSet, 1, &val[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 }
 }
 
 // __<dim_name>_LOC_VALS (for time)
 for( unsigned int i = 0; i != dimNamesSz; i++ )
 {
 if( dimNames[i] == "time" || dimNames[i] == "Time" || dimNames[i] == "t" )
 {
 std::vector< int > val;
 if( !tstep_nums.empty() )
 val = tstep_nums;
 else
 {
 // some files might have Time dimension as 0, it will not appear in any
 // variables, so skip it
 if( tVals.empty() ) continue;
 val.resize( tVals.size() );
 for( unsigned int j = 0; j != tVals.size(); j++ )
 val[j] = j;
 }
 Tag tagh = 0;
 std::stringstream ss_tag_name;
 ss_tag_name << "__" << dimNames[i] << "_LOC_VALS";
 tag_name = ss_tag_name.str();
 rval = mbImpl->tag_get_handle( tag_name.c_str(), val.size(), MB_TYPE_INTEGER, tagh,
 MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( tagh, &_fileSet, 1, &val[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 }
 }
 
 // __<var_name>_DIMS
 for( mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter )
 {
 Tag varNamesDimsTag = 0;
 std::stringstream ss_tag_name;
 ss_tag_name << "__" << mapIter->first << "_DIMS";
 tag_name = ss_tag_name.str();
 unsigned int varDimSz = varInfo[mapIter->first].varDims.size();
 if( varDimSz == 0 ) continue;
 std::vector< Tag > varDimTags( varDimSz );
 for( unsigned int i = 0; i != varDimSz; i++ )
 {
 Tag tmptag = 0;
 std::string tmptagname = dimNames[varInfo[mapIter->first].varDims[i]];
 rval = mbImpl->tag_get_handle( tmptagname.c_str(), 0, MB_TYPE_OPAQUE, tmptag, MB_TAG_ANY );MB_CHK_SET_ERR( rval, "Trouble getting tag " << tmptagname );
 varDimTags[i] = tmptag;
 }
 // rval = mbImpl->tag_get_handle(tag_name.c_str(), varDimSz, MB_TYPE_HANDLE,
 // varNamesDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); We should not use MB_TYPE_HANDLE for Tag
 // here. Tag is a pointer, which is 4 bytes on 32 bit machines and 8 bytes on 64 bit
 // machines. Normally, entity handle is 8 bytes on 64 bit machines, but it can also be
 // configured to 4 bytes.
 rval = mbImpl->tag_get_handle( tag_name.c_str(), varDimSz * sizeof( Tag ), MB_TYPE_OPAQUE, varNamesDimsTag,
 MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( varNamesDimsTag, &_fileSet, 1, &( varDimTags[0] ) );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 }
 
 // <PARTITION_METHOD>
 Tag part_tag = scdi->part_method_tag();
 if( !part_tag ) MB_SET_ERR( MB_FAILURE, "Trouble getting PARTITION_METHOD tag" );
 rval = mbImpl->tag_set_data( part_tag, &_fileSet, 1, &partMethod );MB_CHK_SET_ERR( rval, "Trouble setting data to PARTITION_METHOD tag" );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__GLOBAL_ATTRIBS>
 tag_name = "__GLOBAL_ATTRIBS";
 Tag globalAttTag = 0;
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 std::string gattVal;
 std::vector< int > gattLen;
 rval = create_attrib_string( globalAtts, gattVal, gattLen );MB_CHK_SET_ERR( rval, "Trouble creating global attribute string" );
 const void* gattptr = gattVal.c_str();
 int globalAttSz = gattVal.size();
 rval = mbImpl->tag_set_by_ptr( globalAttTag, &_fileSet, 1, &gattptr, &globalAttSz );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__GLOBAL_ATTRIBS_LEN>
 tag_name = "__GLOBAL_ATTRIBS_LEN";
 Tag globalAttLenTag = 0;
 if( gattLen.size() == 0 ) gattLen.push_back( 0 );
 rval = mbImpl->tag_get_handle( tag_name.c_str(), gattLen.size(), MB_TYPE_INTEGER, globalAttLenTag,
 MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( globalAttLenTag, &_fileSet, 1, &gattLen[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // __<var_name>_ATTRIBS and __<var_name>_ATTRIBS_LEN
 for( mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter )
 {
 std::stringstream ssTagName;
 ssTagName << "__" << mapIter->first << "_ATTRIBS";
 tag_name = ssTagName.str();
 Tag varAttTag = 0;
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 
 std::string varAttVal;
 std::vector< int > varAttLen;
 if( mapIter->second.numAtts < 1 )
 {
 if( dummyVarNames.find( mapIter->first ) != dummyVarNames.end() )
 {
 // This variable is a dummy coordinate variable
 varAttVal = "DUMMY_VAR";
 }
 else
 {
 // This variable has no attributes
 varAttVal = "NO_ATTRIBS";
 }
 }
 else
 {
 rval = create_attrib_string( mapIter->second.varAtts, varAttVal, varAttLen );MB_CHK_SET_ERR( rval, "Trouble creating attribute string for variable " << mapIter->first );
 }
 const void* varAttPtr = varAttVal.c_str();
 int varAttSz = varAttVal.size();
 if( 0 == varAttSz ) varAttSz = 1;
 rval = mbImpl->tag_set_by_ptr( varAttTag, &_fileSet, 1, &varAttPtr, &varAttSz );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 ssTagName << "_LEN";
 tag_name = ssTagName.str();
 Tag varAttLenTag = 0;
 if( 0 == varAttLen.size() ) varAttLen.push_back( 0 );
 rval = mbImpl->tag_get_handle( tag_name.c_str(), varAttLen.size(), MB_TYPE_INTEGER, varAttLenTag,
 MB_TAG_SPARSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 rval = mbImpl->tag_set_data( varAttLenTag, &_fileSet, 1, &varAttLen[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 }
 
 // <__VAR_NAMES_LOCATIONS>
 tag_name = "__VAR_NAMES_LOCATIONS";
 Tag varNamesLocsTag = 0;
 std::vector< int > varNamesLocs( varInfo.size() );
 rval = mbImpl->tag_get_handle( tag_name.c_str(), varNamesLocs.size(), MB_TYPE_INTEGER, varNamesLocsTag,
 MB_TAG_CREAT | MB_TAG_SPARSE );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 for( mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter )
 {
 varNamesLocs[std::distance( varInfo.begin(), mapIter )] = mapIter->second.entLoc;
 }
 rval = mbImpl->tag_set_data( varNamesLocsTag, &_fileSet, 1, &varNamesLocs[0] );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 // <__MESH_TYPE>
 Tag meshTypeTag = 0;
 tag_name = "__MESH_TYPE";
 std::string meshTypeName = get_mesh_type_name();
 
 rval = mbImpl->tag_get_handle( tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating conventional tag " << tag_name );
 ptr = meshTypeName.c_str();
 int leng = meshTypeName.size();
 rval = mbImpl->tag_set_by_ptr( meshTypeTag, &_fileSet, 1, &ptr, &leng );MB_CHK_SET_ERR( rval, "Trouble setting data to conventional tag " << tag_name );
 dbgOut.tprintf( 2, "Conventional tag %s created\n", tag_name.c_str() );
 
 return MB_SUCCESS;
}

References _fileSet, _readNC, create_attrib_string(), moab::ReadNC::dbgOut, moab::ReadNC::dimLens, moab::ReadNC::dimNames, dummyVarNames, ErrorCode, get_mesh_type_name(), moab::ReadNC::globalAtts, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_ANY, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, moab::ReadNC::mbImpl, nTimeSteps, moab::ScdInterface::part_method_tag(), moab::ReadNC::partMethod, moab::ReadNC::scdi, moab::Interface::tag_get_handle(), moab::Interface::tag_set_by_ptr(), moab::Interface::tag_set_data(), moab::DebugOutput::tprintf(), tVals, and moab::ReadNC::varInfo.

Referenced by moab::ReadNC::load_file().

create_dummy_variables()

ErrorCode moab::NCHelper::create_dummy_variables ( )

protected

For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create a dummy variable with a sparse tag to store the dimension length.

Definition at line 819 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 std::vector< std::string >& dimNames = _readNC->dimNames;
 std::vector< int >& dimLens = _readNC->dimLens;
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 // Hack: look at all dimensions, and see if we have one that does not appear in the list of
 // varInfo names Right now, candidates are from unstructured meshes, such as ncol (HOMME) and
 // nCells (MPAS) For each of them, create a dummy coordinate variable with a sparse tag to store
 // the dimension length
 for( unsigned int i = 0; i < dimNames.size(); i++ )
 {
 // If there is a variable with this dimension name, skip
 if( varInfo.find( dimNames[i] ) != varInfo.end() ) continue;
 
 // Create a dummy coordinate variable
 int sizeTotalVar = varInfo.size();
 std::string var_name( dimNames[i] );
 ReadNC::VarData& data = varInfo[var_name];
 data.varName = var_name;
 data.varId = sizeTotalVar;
 data.varTags.resize( 1, 0 );
 data.varDataType = NC_INT;
 data.varDims.resize( 1 );
 data.varDims[0] = (int)i;
 data.numAtts = 0;
 data.entLoc = ReadNC::ENTLOCSET;
 dummyVarNames.insert( var_name );
 dbgOut.tprintf( 2, "Dummy coordinate variable created for dimension %s\n", var_name.c_str() );
 
 // Create a corresponding sparse tag
 Tag tagh;
 ErrorCode rval = mbImpl->tag_get_handle( var_name.c_str(), 0, MB_TYPE_INTEGER, tagh,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating tag for dummy coordinate variable " << var_name );
 
 // Tag value is the dimension length
 const void* ptr = &dimLens[i];
 // Tag size is 1
 int size = 1;
 rval = mbImpl->tag_set_by_ptr( tagh, &_fileSet, 1, &ptr, &size );MB_CHK_SET_ERR( rval, "Trouble setting tag data for dummy coordinate variable " << var_name );
 
 dbgOut.tprintf( 2, "Sparse tag created for dimension %s\n", var_name.c_str() );
 }
 
 return MB_SUCCESS;
}

References _fileSet, _readNC, moab::ReadNC::dbgOut, moab::ReadNC::dimLens, moab::ReadNC::dimNames, dummyVarNames, moab::ReadNC::VarData::entLoc, moab::ReadNC::ENTLOCSET, ErrorCode, MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_INTEGER, moab::ReadNC::mbImpl, moab::ReadNC::VarData::numAtts, size, moab::Interface::tag_get_handle(), moab::Interface::tag_set_by_ptr(), moab::DebugOutput::tprintf(), moab::ReadNC::VarData::varDataType, moab::ReadNC::VarData::varDims, moab::ReadNC::VarData::varId, moab::ReadNC::varInfo, moab::ReadNC::VarData::varName, and moab::ReadNC::VarData::varTags.

Referenced by moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

create_mesh()

virtual ErrorCode moab::NCHelper::create_mesh ( Range &  faces )

pure virtual

Implemented in moab::NCHelperScrip, moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, moab::NCHelperESMF, moab::NCHelperDomain, and moab::ScdNCHelper.

Referenced by moab::ReadNC::load_file().

get_default_ncformat_options()

std::string moab::NCHelper::get_default_ncformat_options ( ReadNC::NCFormatType  format )

static

Get appropriate format to read the file.

Get appropriate file read options depending on the format of the NC file.

Definition at line 66 of file NCHelper.cpp.

{
 switch( format )
 {
 case moab::ReadNC::NC_FORMAT_GCRM: // GCRM format reader
 case moab::ReadNC::NC_FORMAT_MPAS: // MPAS format reader
 return "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;"
 "PARALLEL_RESOLVE_SHARED_ENTS;NO_EDGES;NO_MIXED_ELEMENTS;VARIABLE=;";
 case moab::ReadNC::NC_FORMAT_SCRIP: // SCRIP format reader
 return "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;";
 case moab::ReadNC::NC_FORMAT_ESMF: // ESMF unstructured format reader
 return "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;PARALLEL_RESOLVE_SHARED_ENTS;VARIABLE=;";
 case moab::ReadNC::NC_FORMAT_DOMAIN: // Climate Domain reader
 return "PARALLEL=READ_PART;PARTITION_METHOD=SQIJ;VARIABLE=;";
 case moab::ReadNC::NC_FORMAT_HOMME: // HOMME format reader
 return "PARALLEL=READ_PART;PARTITION_METHOD=TRIVIAL;PARALLEL_RESOLVE_SHARED_ENTS;";
 case moab::ReadNC::NC_FORMAT_EULER: // Euler format reader
 case moab::ReadNC::NC_FORMAT_FV: // FV climate format reader
 return "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;"
 "PARTITION_METHOD=SQIJ;VARIABLE=;";
 default:
 return "PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN;PARALLEL_RESOLVE_SHARED_ENTS;";
 }
}

References moab::ReadNC::NC_FORMAT_DOMAIN, moab::ReadNC::NC_FORMAT_ESMF, moab::ReadNC::NC_FORMAT_EULER, moab::ReadNC::NC_FORMAT_FV, moab::ReadNC::NC_FORMAT_GCRM, moab::ReadNC::NC_FORMAT_HOMME, moab::ReadNC::NC_FORMAT_MPAS, and moab::ReadNC::NC_FORMAT_SCRIP.

get_mesh_type_name()

virtual std::string moab::NCHelper::get_mesh_type_name ( )

pure virtual

Implemented in moab::NCHelperScrip, moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, moab::NCHelperFV, moab::NCHelperEuler, moab::NCHelperESMF, and moab::NCHelperDomain.

Referenced by create_conventional_tags().

get_nc_format()

ReadNC::NCFormatType moab::NCHelper::get_nc_format ( ReadNC *  readNC, int  fileId  )

static

Get appropriate format to read the file.

Definition at line 24 of file NCHelper.cpp.

{
 // Check if CF convention is being followed
 bool is_CF = false;
 
 std::map< std::string, ReadNC::AttData >& globalAtts = readNC->globalAtts;
 std::map< std::string, ReadNC::AttData >::iterator attIt = globalAtts.find( "conventions" );
 if( attIt == globalAtts.end() ) attIt = globalAtts.find( "Conventions" );
 
 if( attIt != globalAtts.end() )
 {
 unsigned int sz = attIt->second.attLen;
 std::string att_data;
 att_data.resize( sz + 1 );
 att_data[sz] = '\000';
 int success =
 NCFUNC( get_att_text )( fileId, attIt->second.attVarId, attIt->second.attName.c_str(), &att_data[0] );
 if( 0 == success && att_data.find( "CF" ) != std::string::npos ) is_CF = true;
 }
 
 // Depending on the format, update FileOptions as well
 if( NCHelperMPAS::can_read_file( readNC ) )
 return ReadNC::NC_FORMAT_MPAS;
 else if( NCHelperScrip::can_read_file( readNC, fileId ) )
 return ReadNC::NC_FORMAT_SCRIP;
 else if( NCHelperESMF::can_read_file( readNC ) )
 return ReadNC::NC_FORMAT_ESMF;
 else if( NCHelperDomain::can_read_file( readNC, fileId ) && is_CF )
 return ReadNC::NC_FORMAT_DOMAIN;
 else if( NCHelperHOMME::can_read_file( readNC, fileId ) )
 return ReadNC::NC_FORMAT_HOMME;
 else if( NCHelperEuler::can_read_file( readNC, fileId ) && is_CF )
 return ReadNC::NC_FORMAT_EULER;
 else if( NCHelperGCRM::can_read_file( readNC ) )
 return ReadNC::NC_FORMAT_GCRM;
 else if( NCHelperFV::can_read_file( readNC, fileId ) && is_CF )
 return ReadNC::NC_FORMAT_FV;
 else // Unknown NetCDF grid (will fill this in later for POP, CICE and CLM)
 return ReadNC::NC_FORMAT_UNKNOWN_TYPE;
}

References moab::NCHelperESMF::can_read_file(), moab::NCHelperGCRM::can_read_file(), moab::NCHelperMPAS::can_read_file(), moab::NCHelperDomain::can_read_file(), moab::NCHelperEuler::can_read_file(), moab::NCHelperFV::can_read_file(), moab::NCHelperHOMME::can_read_file(), moab::NCHelperScrip::can_read_file(), moab::ReadNC::globalAtts, moab::ReadNC::NC_FORMAT_DOMAIN, moab::ReadNC::NC_FORMAT_ESMF, moab::ReadNC::NC_FORMAT_EULER, moab::ReadNC::NC_FORMAT_FV, moab::ReadNC::NC_FORMAT_GCRM, moab::ReadNC::NC_FORMAT_HOMME, moab::ReadNC::NC_FORMAT_MPAS, moab::ReadNC::NC_FORMAT_SCRIP, moab::ReadNC::NC_FORMAT_UNKNOWN_TYPE, and NCFUNC.

Referenced by get_nc_helper().

get_nc_helper()

NCHelper * moab::NCHelper::get_nc_helper ( ReadNC *  readNC, int  fileId, const FileOptions &  opts, EntityHandle  fileSet  )

static

Get appropriate helper instance for ReadNC class.

Definition at line 91 of file NCHelper.cpp.

{
 ReadNC::NCFormatType nctype = NCHelper::get_nc_format( readNC, fileId );
 
 switch( nctype )
 {
 case ReadNC::NC_FORMAT_MPAS: // MPAS format reader
 return new( std::nothrow ) NCHelperMPAS( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_SCRIP: // SCRIP format reader
 // SCRIP can be CF or non CF, if it comes from MPAS :)
 return new( std::nothrow ) NCHelperScrip( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_ESMF: // ESMF unstructured format reader
 return new( std::nothrow ) NCHelperESMF( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_DOMAIN: // Climate Domain reader
 return new( std::nothrow ) NCHelperDomain( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_HOMME: // HOMME format reader
 // For a HOMME connectivity file, there might be no CF convention
 return new( std::nothrow ) NCHelperHOMME( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_GCRM: // GCRM format reader
 return new( std::nothrow ) NCHelperGCRM( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_EULER: // Euler format reader
 return new( std::nothrow ) NCHelperEuler( readNC, fileId, opts, fileSet );
 case ReadNC::NC_FORMAT_FV: // FV climate format reader
 return new( std::nothrow ) NCHelperFV( readNC, fileId, opts, fileSet );
 default: // Unknown NetCDF grid (will fill this in later for POP, CICE and CLM)
 return nullptr;
 }
}

References get_nc_format(), moab::ReadNC::NC_FORMAT_DOMAIN, moab::ReadNC::NC_FORMAT_ESMF, moab::ReadNC::NC_FORMAT_EULER, moab::ReadNC::NC_FORMAT_FV, moab::ReadNC::NC_FORMAT_GCRM, moab::ReadNC::NC_FORMAT_HOMME, moab::ReadNC::NC_FORMAT_MPAS, and moab::ReadNC::NC_FORMAT_SCRIP.

Referenced by moab::ReadNC::load_file().

get_tag_to_nonset()

ErrorCode moab::NCHelper::get_tag_to_nonset ( ReadNC::VarData &  var_data, int  tstep_num, Tag &  tagh, int  num_lev  )

protected

Definition at line 694 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 DebugOutput& dbgOut = _readNC->dbgOut;
 int& tStepBase = _readNC->tStepBase;
 
 if( tStepBase > 0 ) tstep_num += tStepBase;
 
 std::ostringstream tag_name;
 tag_name << var_data.varName << tstep_num;
 
 ErrorCode rval = MB_SUCCESS;
 tagh = 0;
 switch( var_data.varDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), num_lev, MB_TYPE_OPAQUE, tagh,
 MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 case NC_SHORT:
 case NC_INT:
 case NC_INT64:
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), num_lev, MB_TYPE_INTEGER, tagh,
 MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 case NC_FLOAT:
 case NC_DOUBLE:
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), num_lev, MB_TYPE_DOUBLE, tagh,
 MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << var_data.varName );
 }
 
 dbgOut.tprintf( 2, "Tag %s created\n", tag_name.str().c_str() );
 
 return rval;
}

References _readNC, moab::ReadNC::dbgOut, ErrorCode, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, moab::ReadNC::mbImpl, moab::Interface::tag_get_handle(), moab::DebugOutput::tprintf(), moab::ReadNC::tStepBase, moab::ReadNC::VarData::varDataType, and moab::ReadNC::VarData::varName.

Referenced by moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), and moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate().

get_tag_to_set()

ErrorCode moab::NCHelper::get_tag_to_set ( ReadNC::VarData &  var_data, int  tstep_num, Tag &  tagh  )

protected

Definition at line 651 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 DebugOutput& dbgOut = _readNC->dbgOut;
 int& tStepBase = _readNC->tStepBase;
 
 if( tStepBase > 0 ) tstep_num += tStepBase;
 
 std::ostringstream tag_name;
 if( var_data.has_tsteps )
 tag_name << var_data.varName << tstep_num;
 else
 tag_name << var_data.varName;
 
 ErrorCode rval = MB_SUCCESS;
 tagh = 0;
 switch( var_data.varDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), 0, MB_TYPE_OPAQUE, tagh,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 case NC_SHORT:
 case NC_INT:
 case NC_INT64: // this is a big stretch; we should introduce LONG tag
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), 0, MB_TYPE_INTEGER, tagh,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 case NC_FLOAT:
 case NC_DOUBLE:
 rval = mbImpl->tag_get_handle( tag_name.str().c_str(), 0, MB_TYPE_DOUBLE, tagh,
 MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble creating tag " << tag_name.str() );
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << var_data.varName );
 }
 
 dbgOut.tprintf( 2, "Tag %s created\n", tag_name.str().c_str() );
 
 return rval;
}

References _readNC, moab::ReadNC::dbgOut, ErrorCode, moab::ReadNC::VarData::has_tsteps, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TAG_VARLEN, MB_TYPE_DOUBLE, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, moab::ReadNC::mbImpl, moab::Interface::tag_get_handle(), moab::DebugOutput::tprintf(), moab::ReadNC::tStepBase, moab::ReadNC::VarData::varDataType, and moab::ReadNC::VarData::varName.

Referenced by read_variables_to_set_allocate().

init_mesh_vals()

virtual ErrorCode moab::NCHelper::init_mesh_vals ( )

pure virtual

Interfaces to be implemented in child classes.

Implemented in moab::NCHelperScrip, moab::NCHelperMPAS, moab::NCHelperHOMME, moab::NCHelperGCRM, moab::NCHelperFV, moab::NCHelperEuler, moab::NCHelperESMF, and moab::NCHelperDomain.

Referenced by moab::ReadNC::load_file().

read_coordinate()

ErrorCode moab::NCHelper::read_coordinate ( const char *  var_name, int  lmin, int  lmax, std::vector< double > &  cvals  )

protected

Definition at line 619 of file NCHelper.cpp.

{
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 std::map< std::string, ReadNC::VarData >::iterator vmit = varInfo.find( var_name );
 if( varInfo.end() == vmit ) MB_SET_ERR( MB_FAILURE, "Couldn't find variable " << var_name );
 
 assert( lmin >= 0 && lmax >= lmin );
 NCDF_SIZE tstart = lmin;
 NCDF_SIZE tcount = lmax - lmin + 1;
 NCDF_DIFF dum_stride = 1;
 int success;
 
 // Check size
 if( (std::size_t)tcount != cvals.size() ) cvals.resize( tcount );
 
 // Check to make sure it's a float or double
 switch( ( *vmit ).second.varDataType )
 {
 case NC_FLOAT:
 case NC_DOUBLE:
 // Read float as double
 success =
 NCFUNCAG( _vars_double )( _fileId, ( *vmit ).second.varId, &tstart, &tcount, &dum_stride, &cvals[0] );
 if( success ) MB_SET_ERR( MB_FAILURE, "Failed to read float/double data for variable " << var_name );
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << var_name );
 }
 
 return MB_SUCCESS;
}

References _fileId, _readNC, MB_SET_ERR, MB_SUCCESS, NCDF_DIFF, NCDF_SIZE, NCFUNCAG, and moab::ReadNC::varInfo.

Referenced by moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

read_variables()

virtual ErrorCode moab::NCHelper::read_variables ( std::vector< std::string > &  var_names, std::vector< int > &  tstep_nums  )

pure virtual

Implemented in moab::UcdNCHelper, and moab::ScdNCHelper.

Referenced by moab::ReadNC::load_file().

read_variables_setup()

ErrorCode moab::NCHelper::read_variables_setup ( std::vector< std::string > &  var_names, std::vector< int > &  tstep_nums, std::vector< ReadNC::VarData > &  vdatas, std::vector< ReadNC::VarData > &  vsetdatas  )

protected

Separate set and non-set variables (common to scd mesh and ucd mesh)

Definition at line 421 of file NCHelper.cpp.

{
 std::map< std::string, ReadNC::VarData >& varInfo = _readNC->varInfo;
 std::vector< std::string >& dimNames = _readNC->dimNames;
 
 std::map< std::string, ReadNC::VarData >::iterator mit;
 
 // If empty read them all (except ignored variables)
 if( var_names.empty() )
 {
 for( mit = varInfo.begin(); mit != varInfo.end(); ++mit )
 {
 ReadNC::VarData vd = ( *mit ).second;
 
 // If read all variables at once, skip ignored ones
 if( ignoredVarNames.find( vd.varName ) != ignoredVarNames.end() ) continue;
 
 // Coordinate variables (include dummy ones) were read to the file set by default
 if( std::find( dimNames.begin(), dimNames.end(), vd.varName ) != dimNames.end() ) continue;
 
 if( vd.entLoc == ReadNC::ENTLOCSET )
 vsetdatas.push_back( vd );
 else
 vdatas.push_back( vd );
 }
 }
 else
 {
 // Read specified variables (might include ignored ones)
 for( unsigned int i = 0; i < var_names.size(); i++ )
 {
 mit = varInfo.find( var_names[i] );
 if( mit != varInfo.end() )
 {
 ReadNC::VarData vd = ( *mit ).second;
 
 // Upon creation of dummy coordinate variables, tag values have already been set
 if( dummyVarNames.find( vd.varName ) != dummyVarNames.end() ) continue;
 
 if( vd.entLoc == ReadNC::ENTLOCSET )
 vsetdatas.push_back( vd );
 else
 vdatas.push_back( vd );
 }
 else
 {
 MB_SET_ERR( MB_FAILURE, "Couldn't find specified variable " << var_names[i] );
 }
 }
 }
 
 if( tstep_nums.empty() && nTimeSteps > 0 )
 {
 // No timesteps input, get them all
 for( int i = 0; i < nTimeSteps; i++ )
 tstep_nums.push_back( i );
 }
 
 if( !tstep_nums.empty() )
 {
 for( unsigned int i = 0; i < vdatas.size(); i++ )
 {
 vdatas[i].varTags.resize( tstep_nums.size(), 0 );
 vdatas[i].varDatas.resize( tstep_nums.size() );
 // NC reader assumes that non-set variables always have timesteps
 assert( std::find( vdatas[i].varDims.begin(), vdatas[i].varDims.end(), tDim ) != vdatas[i].varDims.end() );
 vdatas[i].has_tsteps = true;
 }
 
 for( unsigned int i = 0; i < vsetdatas.size(); i++ )
 {
 if( ( std::find( vsetdatas[i].varDims.begin(), vsetdatas[i].varDims.end(), tDim ) !=
 vsetdatas[i].varDims.end() ) &&
 ( vsetdatas[i].varName != dimNames[tDim] ) )
 {
 // Set variables with timesteps: e.g. xtime(Time) or xtime(Time, StrLen)
 vsetdatas[i].varTags.resize( tstep_nums.size(), 0 );
 vsetdatas[i].varDatas.resize( tstep_nums.size() );
 vsetdatas[i].has_tsteps = true;
 }
 else
 {
 // Set variables without timesteps: no time dimension, or time itself
 vsetdatas[i].varTags.resize( 1, 0 );
 vsetdatas[i].varDatas.resize( 1 );
 vsetdatas[i].has_tsteps = false;
 }
 }
 }
 
 return MB_SUCCESS;
}

References _readNC, moab::ReadNC::dimNames, dummyVarNames, moab::ReadNC::VarData::entLoc, moab::ReadNC::ENTLOCSET, ignoredVarNames, MB_SET_ERR, MB_SUCCESS, nTimeSteps, tDim, moab::ReadNC::varInfo, and moab::ReadNC::VarData::varName.

Referenced by moab::ScdNCHelper::read_variables(), and moab::UcdNCHelper::read_variables().

read_variables_to_set()

ErrorCode moab::NCHelper::read_variables_to_set ( std::vector< ReadNC::VarData > &  vdatas, std::vector< int > &  tstep_nums  )

protected

Read set variables (common to scd mesh and ucd mesh)

Definition at line 517 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 ErrorCode rval = read_variables_to_set_allocate( vdatas, tstep_nums );MB_CHK_SET_ERR( rval, "Trouble allocating space to read set variables" );
 
 // Finally, read into that space
 int success;
 for( unsigned int i = 0; i < vdatas.size(); i++ )
 {
 // Note, for set variables without timesteps, loop one time and then break
 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 {
 void* data = vdatas[i].varDatas[t];
 
 // Set variables with timesteps, e.g. xtime(Time) or xtime(Time, StrLen)
 if( vdatas[i].has_tsteps )
 {
 // Set readStart for each timestep along time dimension
 vdatas[i].readStarts[0] = tstep_nums[t];
 }
 
 switch( vdatas[i].varDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 success = NCFUNCAG( _vara_text )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 &vdatas[i].readCounts[0], (char*)data );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read byte/char data for variable " << vdatas[i].varName );
 break;
 case NC_SHORT:
 case NC_INT:
 success = NCFUNCAG( _vara_int )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 &vdatas[i].readCounts[0], (int*)data );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read short/int data for variable " << vdatas[i].varName );
 break;
 case NC_INT64:
 success = NCFUNCAG( _vara_long )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 &vdatas[i].readCounts[0], (long*)data );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read long data for variable " << vdatas[i].varName );
 break;
 case NC_FLOAT:
 case NC_DOUBLE:
 success = NCFUNCAG( _vara_double )( _fileId, vdatas[i].varId, &vdatas[i].readStarts[0],
 &vdatas[i].readCounts[0], (double*)data );
 if( success )
 MB_SET_ERR( MB_FAILURE, "Failed to read float/double data for variable " << vdatas[i].varName );
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
 }
 
 dbgOut.tprintf( 2, "Setting data for variable %s, time step %d\n", vdatas[i].varName.c_str(),
 tstep_nums[t] );
 rval = mbImpl->tag_set_by_ptr( vdatas[i].varTags[t], &_fileSet, 1, &data, &vdatas[i].sz );MB_CHK_SET_ERR( rval, "Trouble setting tag data for variable " << vdatas[i].varName );
 
 // Memory pointed by pointer data can be deleted, as tag_set_by_ptr() has already copied
 // the tag values
 switch( vdatas[i].varDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 delete[](char*)data;
 break;
 case NC_SHORT:
 case NC_INT:
 delete[](int*)data;
 break;
 case NC_INT64:
 delete[](long*)data;
 break;
 case NC_FLOAT:
 case NC_DOUBLE:
 delete[](double*)data;
 break;
 default:
 break;
 }
 vdatas[i].varDatas[t] = NULL;
 
 // Loop continues only for set variables with timesteps, e.g. xtime(Time) or xtime(Time,
 // StrLen)
 if( !vdatas[i].has_tsteps ) break;
 }
 }
 
 // Debug output, if requested
 if( 1 == dbgOut.get_verbosity() )
 {
 dbgOut.printf( 1, "Read variables: %s", vdatas.begin()->varName.c_str() );
 for( unsigned int i = 1; i < vdatas.size(); i++ )
 dbgOut.printf( 1, ", %s ", vdatas[i].varName.c_str() );
 dbgOut.tprintf( 1, "\n" );
 }
 
 return rval;
}

References _fileId, _fileSet, _readNC, moab::ReadNC::dbgOut, ErrorCode, moab::DebugOutput::get_verbosity(), MB_CHK_SET_ERR, MB_SET_ERR, moab::ReadNC::mbImpl, NCFUNCAG, moab::DebugOutput::printf(), read_variables_to_set_allocate(), t, moab::Interface::tag_set_by_ptr(), and moab::DebugOutput::tprintf().

Referenced by moab::ScdNCHelper::read_variables(), and moab::UcdNCHelper::read_variables().

read_variables_to_set_allocate()

ErrorCode moab::NCHelper::read_variables_to_set_allocate ( std::vector< ReadNC::VarData > &  vdatas, std::vector< int > &  tstep_nums  )

private

Used by read_variables_to_set()

Definition at line 868 of file NCHelper.cpp.

{
 std::vector< int >& dimLens = _readNC->dimLens;
 DebugOutput& dbgOut = _readNC->dbgOut;
 
 ErrorCode rval = MB_SUCCESS;
 
 for( unsigned int i = 0; i < vdatas.size(); i++ )
 {
 // Set up readStarts and readCounts
 if( vdatas[i].has_tsteps )
 {
 // First: time
 vdatas[i].readStarts.push_back( 0 ); // This value is timestep dependent, will be set later
 vdatas[i].readCounts.push_back( 1 );
 
 // Next: other dimensions
 for( unsigned int idx = 1; idx != vdatas[i].varDims.size(); idx++ )
 {
 vdatas[i].readStarts.push_back( 0 );
 vdatas[i].readCounts.push_back( dimLens[vdatas[i].varDims[idx]] );
 }
 }
 else
 {
 if( vdatas[i].varDims.empty() )
 {
 // Scalar variable
 vdatas[i].readStarts.push_back( 0 );
 vdatas[i].readCounts.push_back( 1 );
 }
 else
 {
 for( unsigned int idx = 0; idx != vdatas[i].varDims.size(); idx++ )
 {
 vdatas[i].readStarts.push_back( 0 );
 vdatas[i].readCounts.push_back( dimLens[vdatas[i].varDims[idx]] );
 }
 }
 }
 
 // Get variable size
 vdatas[i].sz = 1;
 for( std::size_t idx = 0; idx != vdatas[i].readCounts.size(); idx++ )
 vdatas[i].sz *= vdatas[i].readCounts[idx];
 
 // Note, for set variables without timesteps, loop one time and then break
 for( unsigned int t = 0; t < tstep_nums.size(); t++ )
 {
 dbgOut.tprintf( 2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t] );
 
 if( tstep_nums[t] >= dimLens[tDim] )
 {
 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number " << tstep_nums[t] );
 }
 
 // Get the tag to read into
 if( !vdatas[i].varTags[t] )
 {
 rval = get_tag_to_set( vdatas[i], tstep_nums[t], vdatas[i].varTags[t] );MB_CHK_SET_ERR( rval, "Trouble getting tag to set variable " << vdatas[i].varName );
 }
 
 switch( vdatas[i].varDataType )
 {
 case NC_BYTE:
 case NC_CHAR:
 vdatas[i].varDatas[t] = new char[vdatas[i].sz];
 break;
 case NC_SHORT:
 case NC_INT:
 vdatas[i].varDatas[t] = new int[vdatas[i].sz];
 break;
 case NC_INT64:
 vdatas[i].varDatas[t] = new long[vdatas[i].sz];
 break;
 case NC_FLOAT:
 case NC_DOUBLE:
 vdatas[i].varDatas[t] = new double[vdatas[i].sz];
 break;
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected data type for variable " << vdatas[i].varName );
 }
 
 // Loop continues only for set variables with timesteps, e.g. xtime(Time) or xtime(Time,
 // StrLen)
 if( !vdatas[i].has_tsteps ) break;
 }
 }
 
 return rval;
}

References _readNC, moab::ReadNC::dbgOut, moab::ReadNC::dimLens, ErrorCode, get_tag_to_set(), MB_CHK_SET_ERR, MB_INDEX_OUT_OF_RANGE, MB_SET_ERR, MB_SUCCESS, t, tDim, and moab::DebugOutput::tprintf().

Referenced by read_variables_to_set().

update_time_tag_vals()

ErrorCode moab::NCHelper::update_time_tag_vals

(

)

Update time tag values if timesteps spread across files.

Definition at line 372 of file NCHelper.cpp.

{
 Interface*& mbImpl = _readNC->mbImpl;
 std::vector< std::string >& dimNames = _readNC->dimNames;
 
 ErrorCode rval;
 
 // The time tag might be a dummy one (e.g. 'Time' for MPAS)
 std::string time_tag_name = dimNames[tDim];
 if( dummyVarNames.find( time_tag_name ) != dummyVarNames.end() ) return MB_SUCCESS;
 
 Tag time_tag = 0;
 const void* data = NULL;
 int time_tag_size = 0;
 rval = mbImpl->tag_get_handle( time_tag_name.c_str(), 0, MB_TYPE_DOUBLE, time_tag, MB_TAG_VARLEN );MB_CHK_SET_ERR( rval, "Trouble getting tag " << time_tag_name );
 rval = mbImpl->tag_get_by_ptr( time_tag, &_fileSet, 1, &data, &time_tag_size );MB_CHK_SET_ERR( rval, "Trouble getting data of tag " << time_tag_name );
 const double* time_tag_vals = static_cast< const double* >( data );
 
 // Merge tVals (read from current file) to existing time tag
 // Assume that time_tag_vals and tVals are both sorted
 std::vector< double > merged_time_vals;
 merged_time_vals.reserve( time_tag_size + nTimeSteps );
 int i = 0;
 int j = 0;
 
 // Merge time values from time_tag_vals and tVals
 while( i < time_tag_size && j < nTimeSteps )
 {
 if( time_tag_vals[i] < tVals[j] )
 merged_time_vals.push_back( time_tag_vals[i++] );
 else
 merged_time_vals.push_back( tVals[j++] );
 }
 
 // Append remaining time values of time_tag_vals (if any)
 while( i < time_tag_size )
 merged_time_vals.push_back( time_tag_vals[i++] );
 
 // Append remaining time values of tVals (if any)
 while( j < nTimeSteps )
 merged_time_vals.push_back( tVals[j++] );
 
 data = &merged_time_vals[0];
 time_tag_size = merged_time_vals.size();
 rval = mbImpl->tag_set_by_ptr( time_tag, &_fileSet, 1, &data, &time_tag_size );MB_CHK_SET_ERR( rval, "Trouble setting data to tag " << time_tag_name );
 
 return MB_SUCCESS;
}

References _fileSet, _readNC, moab::ReadNC::dimNames, dummyVarNames, ErrorCode, MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_VARLEN, MB_TYPE_DOUBLE, moab::ReadNC::mbImpl, nTimeSteps, moab::Interface::tag_get_by_ptr(), moab::Interface::tag_get_handle(), moab::Interface::tag_set_by_ptr(), tDim, and tVals.

Referenced by moab::ReadNC::load_file().

Member Data Documentation

_fileId

int moab::NCHelper::_fileId

protected

Cache some information from ReadNC.

Definition at line 109 of file NCHelper.hpp.

Referenced by create_attrib_string(), moab::NCHelperMPAS::create_gather_set_cells(), moab::NCHelperGCRM::create_gather_set_edges(), moab::NCHelperMPAS::create_gather_set_edges(), moab::NCHelperGCRM::create_gather_set_vertices(), moab::NCHelperMPAS::create_gather_set_vertices(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::NCHelperDomain::create_mesh(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperGCRM::create_padded_gather_set_cells(), moab::NCHelperMPAS::create_padded_gather_set_cells(), moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), read_coordinate(), moab::ScdNCHelper::read_scd_variables_to_nonset(), moab::NCHelperGCRM::read_ucd_variables_to_nonset(), moab::NCHelperHOMME::read_ucd_variables_to_nonset(), moab::NCHelperMPAS::read_ucd_variables_to_nonset(), and read_variables_to_set().

_fileSet

EntityHandle moab::NCHelper::_fileSet

protected

Definition at line 111 of file NCHelper.hpp.

Referenced by moab::ScdNCHelper::check_existing_mesh(), moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), create_conventional_tags(), create_dummy_variables(), moab::NCHelperESMF::create_local_cells(), moab::NCHelperMPAS::create_local_cells(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperDomain::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), moab::ScdNCHelper::create_quad_coordinate_tag(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate(), read_variables_to_set(), and update_time_tag_vals().

_opts

const FileOptions& moab::NCHelper::_opts

protected

Definition at line 110 of file NCHelper.hpp.

Referenced by moab::NCHelperHOMME::create_mesh(), moab::NCHelperEuler::init_mesh_vals(), and moab::NCHelperFV::init_mesh_vals().

_readNC

ReadNC* moab::NCHelper::_readNC

protected

Allow NCHelper to directly access members of ReadNC.

Definition at line 106 of file NCHelper.hpp.

Referenced by moab::ScdNCHelper::check_existing_mesh(), moab::NCHelperGCRM::check_existing_mesh(), moab::NCHelperHOMME::check_existing_mesh(), moab::NCHelperMPAS::check_existing_mesh(), create_conventional_tags(), create_dummy_variables(), moab::NCHelperMPAS::create_gather_set_cells(), moab::NCHelperGCRM::create_gather_set_edges(), moab::NCHelperMPAS::create_gather_set_edges(), moab::NCHelperGCRM::create_gather_set_vertices(), moab::NCHelperMPAS::create_gather_set_vertices(), moab::NCHelperESMF::create_local_cells(), moab::NCHelperMPAS::create_local_cells(), moab::NCHelperGCRM::create_local_edges(), moab::NCHelperMPAS::create_local_edges(), moab::NCHelperESMF::create_local_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperMPAS::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperDomain::create_mesh(), moab::NCHelperESMF::create_mesh(), moab::NCHelperGCRM::create_mesh(), moab::NCHelperHOMME::create_mesh(), moab::NCHelperMPAS::create_mesh(), moab::NCHelperScrip::create_mesh(), moab::NCHelperGCRM::create_padded_gather_set_cells(), moab::NCHelperMPAS::create_padded_gather_set_cells(), moab::NCHelperESMF::create_padded_local_cells(), moab::NCHelperGCRM::create_padded_local_cells(), moab::NCHelperMPAS::create_padded_local_cells(), moab::ScdNCHelper::create_quad_coordinate_tag(), get_tag_to_nonset(), get_tag_to_set(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperESMF::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), moab::NCHelperScrip::init_mesh_vals(), read_coordinate(), moab::ScdNCHelper::read_scd_variables_to_nonset(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset(), moab::NCHelperHOMME::read_ucd_variables_to_nonset(), moab::NCHelperMPAS::read_ucd_variables_to_nonset(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate(), read_variables_setup(), read_variables_to_set(), read_variables_to_set_allocate(), and update_time_tag_vals().

dummyVarNames

std::set< std::string > moab::NCHelper::dummyVarNames

protected

Dummy variables.

Definition at line 126 of file NCHelper.hpp.

Referenced by create_conventional_tags(), create_dummy_variables(), read_variables_setup(), and update_time_tag_vals().

ignoredVarNames

std::set< std::string > moab::NCHelper::ignoredVarNames

protected

Ignored variables.

Definition at line 123 of file NCHelper.hpp.

Referenced by moab::NCHelperMPAS::init_mesh_vals(), moab::NCHelperGCRM::NCHelperGCRM(), moab::NCHelperMPAS::NCHelperMPAS(), and read_variables_setup().

levDim

int moab::NCHelper::levDim

protected

Definition at line 120 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

levVals

std::vector< double > moab::NCHelper::levVals

protected

Definition at line 117 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::create_gather_set_vertices(), moab::NCHelperGCRM::create_local_vertices(), moab::ScdNCHelper::create_mesh(), moab::NCHelperHOMME::create_mesh(), and moab::NCHelperHOMME::init_mesh_vals().

nLevels

int moab::NCHelper::nLevels

protected

Definition at line 114 of file NCHelper.hpp.

Referenced by moab::NCHelperGCRM::create_local_vertices(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), and moab::NCHelperMPAS::init_mesh_vals().

nTimeSteps

int moab::NCHelper::nTimeSteps

protected

Dimensions of time and level.

Definition at line 114 of file NCHelper.hpp.

Referenced by create_conventional_tags(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), read_variables_setup(), and update_time_tag_vals().

tDim

int moab::NCHelper::tDim

protected

Dimension numbers for time and level.

Definition at line 120 of file NCHelper.hpp.

Referenced by moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), moab::ScdNCHelper::read_scd_variables_to_nonset_allocate(), moab::NCHelperGCRM::read_ucd_variables_to_nonset_allocate(), moab::NCHelperHOMME::read_ucd_variables_to_nonset_allocate(), moab::NCHelperMPAS::read_ucd_variables_to_nonset_allocate(), read_variables_setup(), read_variables_to_set_allocate(), and update_time_tag_vals().

tVals

std::vector< double > moab::NCHelper::tVals

protected

Values for time and level.

Definition at line 117 of file NCHelper.hpp.

Referenced by create_conventional_tags(), moab::NCHelperDomain::init_mesh_vals(), moab::NCHelperEuler::init_mesh_vals(), moab::NCHelperFV::init_mesh_vals(), moab::NCHelperGCRM::init_mesh_vals(), moab::NCHelperHOMME::init_mesh_vals(), moab::NCHelperMPAS::init_mesh_vals(), and update_time_tag_vals().

---

The documentation for this class was generated from the following files:

• NCHelper.hpp
• NCHelper.cpp