GCRM for implementing new file readers in MOAB This class is a GCRM for writing new file readers in MOAB. This shows how to efficiently create vertices and elements using the ReadUtilIface class, and to translate indices in connectivity lists into vertex handles created during the read. More...

#include <ReadGCRM.hpp>

Inheritance diagram for moab::ReadGCRM:

List of all members.

Classes
class	AttData
class	VarData
Public Types
enum	EntityLocation { ENTLOCNODE = 0, ENTLOCNSEDGE, ENTLOCEWEDGE, ENTLOCQUAD, ENTLOCSET }
Public Member Functions
virtual ErrorCode	load_file (const char file_name, const EntityHandle file_set, const FileOptions &opts, const SubsetList subset_list=0, const Tag file_id_tag=0)
	Load mesh from a file.
virtual ErrorCode	read_tag_values (const char file_name, const char tag_name, const FileOptions &opts, std::vector< int > &tag_values_out, const SubsetList *subset_list=0)
	Read tag values from a file.
	ReadGCRM (Interface *impl=NULL)
	Constructor.
virtual	~ReadGCRM ()
	Destructor.
Static Public Member Functions
static ReaderIface *	factory (Interface *)
	factory method
Private Member Functions
ErrorCode	read_vertices (int num_verts, EntityHandle &start_vertex, Range &read_ents)
	Read vertex data and create vertices in MOAB database.
ErrorCode	read_elements (int num_elems, EntityHandle start_vertex, EntityHandle &start_elem, Range &read_ents)
	Read element data and create elements in MOAB database.
ErrorCode	create_sets (int num_sets, EntityHandle start_vertex, int num_verts, EntityHandle start_elem, int num_elems, Range &read_ents)
	Read entity set data and create/populate sets in MOAB database.
ErrorCode	process_options (const FileOptions &opts)
	Process options passed into the reader.
void	reset ()
ErrorCode	read_header ()
	read the header information
ErrorCode	get_attributes (int var_id, int num_atts, std::map< std::string, AttData > &atts, const char *prefix="")
	get all global attributes in the file
ErrorCode	get_dimensions (int file_id, std::vector< std::string > &dim_names, std::vector< int > &dim_vals)
	get all dimensions in the file
ErrorCode	get_variables ()
	get the variable names and other info defined for this file
unsigned int	number_dimensions ()
	number of dimensions in this nc file
ErrorCode	get_tag (VarData &var_data, int tstep_num, Tag &tagh, int num_lev)
ErrorCode	create_attrib_string (const std::map< std::string, AttData > &attMap, std::string &attString, std::vector< int > &attLen)
ErrorCode	create_tags (ScdInterface *scdi, EntityHandle file_set, const std::vector< int > &tstep_nums)
Private Attributes
ReadUtilIface *	readMeshIface
int	CPU_WORD_SIZE
int	IO_WORD_SIZE
Interface *	mbImpl
	interface instance
const char *	fileName
int	fileId
	file numbers assigned by netcdf
int	connectId
std::vector< std::string >	dimNames
	dimensions
std::vector< int >	dimVals
std::map< std::string, AttData >	globalAtts
	global attribs
std::map< std::string, VarData >	varInfo
	variable info
int	tMin
int	tMax
std::vector< double >	tVals
	values for t
int	tDim
	dimension numbers for i, j, t
int	numUnLim
	number of the dimension of unlimited dimension, if any
EntityHandle	mCurrentMeshHandle
	Meshset Handle for the mesh that is currently being read.
EntityHandle	startVertex
	starting vertex and element handles for this read
EntityHandle	startElem
Tag	mGlobalIdTag
int	max_line_length
int	max_str_length
Range	initRange
	range of entities in initial mesh, before this read
int	vertexOffset
	offset of first vertex id
DebugOutput	dbgOut
	debug stuff
int	partMethod
	partitioning method
bool	isParallel
	are we reading in parallel?

Detailed Description

GCRM for implementing new file readers in MOAB This class is a GCRM for writing new file readers in MOAB. This shows how to efficiently create vertices and elements using the ReadUtilIface class, and to translate indices in connectivity lists into vertex handles created during the read.

After writing the new reader class, you should also modify src/ReaderWriterSet.cpp, to register the new reader along with the file extensions that it reads. This will turn on automatic creating of this reader based on file extension, which is done in Core::serial_load_file.

Definition at line 66 of file ReadGCRM.hpp.

Member Enumeration Documentation

enum moab::ReadGCRM::EntityLocation

Enumerator:

ENTLOCNODE
ENTLOCNSEDGE
ENTLOCEWEDGE
ENTLOCQUAD
ENTLOCSET

Definition at line 94 of file ReadGCRM.hpp.

{ENTLOCNODE=0, ENTLOCNSEDGE, ENTLOCEWEDGE, ENTLOCQUAD, ENTLOCSET};

Constructor & Destructor Documentation

moab::ReadGCRM::ReadGCRM ( Interface * impl = NULL )

Constructor.

Definition at line 33 of file ReadGCRM.cpp.

                                  :
  CPU_WORD_SIZE(-1), IO_WORD_SIZE(-1), mbImpl(impl), fileId(-1), tMin(-1), tMax(-1), tDim(-1), 
      numUnLim(-1), mCurrentMeshHandle(0), startVertex(0), startElem(0), mGlobalIdTag(0), max_line_length(-1),
      max_str_length(-1), vertexOffset(0), dbgOut(stderr), partMethod(-1), isParallel(false)

#ifdef USE_MPI
, myPcomm(NULL)
#endif
{
  assert(impl != NULL);
  impl->query_interface(readMeshIface);
}

moab::ReadGCRM::~ReadGCRM ( ) [virtual]

Destructor.

Definition at line 46 of file ReadGCRM.cpp.

{
  if (readMeshIface) {
    mbImpl->release_interface(readMeshIface);
    readMeshIface = 0;
  }
}

Member Function Documentation

ErrorCode moab::ReadGCRM::create_attrib_string	(	const std::map< std::string, AttData > &	attMap,
		std::string &	attString,
		std::vector< int > &	attLen
	)		`[private]`

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 postion for each name/data type/ value.

Definition at line 627 of file ReadGCRM.cpp.

                                                                                                                            {
  int success;
  std::stringstream ssAtt;
  unsigned int sz = 0;
  std::map<std::string, 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);
        ERRORS(success, "Failed to read attribute char data.")
        ;
        ssAtt << "char;";
        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);
        ERRORS(success, "Failed to read attribute double data.")
        ;
        ssAtt << "double;";
        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);
        ERRORS(success, "Failed to read attribute float data.")
        ;
        ssAtt << "float;";
        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);
        ERRORS(success, "Failed to read attribute int data.")
        ;
        ssAtt << "int;";
        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);
        ERRORS(success, "Failed to read attribute short data.")
        ;
        ssAtt << "short;";
        break;
      default:
        success = 1;
    }
    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;
}

ErrorCode moab::ReadGCRM::create_sets	(	int	num_sets,
		EntityHandle	start_vertex,
		int	num_verts,
		EntityHandle	start_elem,
		int	num_elems,
		Range &	read_ents
	)		`[private]`

Read entity set data and create/populate sets in MOAB database.

read/create sets

Parameters:

num_sets	Number of sets to be read
start_vertex	Starting vertex handle
num_verts	Total number of vertices read from file
start_elem	Starting element handle
num_elems	Total number of elements read from file
read_ents	Range storing all entities read from this file

Definition at line 227 of file ReadGCRM.cpp.

{ 
  ErrorCode result = MB_SUCCESS;
  EntityHandle this_set;
  
  for (int i = 0; i < num_sets; i++) {
      // create set
    result = mbImpl->create_meshset(MESHSET_SET, this_set);
    if (MB_SUCCESS != result) {
      readMeshIface->report_error("%s: Trouble creating set.\n", fileName);
      return result;
    }

    Range set_ents;
      // read/compute what's in this set; REMEMBER TO CONVERT THESE TO MOAB HANDLES

      // add them to the set
    result = mbImpl->add_entities(this_set, set_ents);
    if (MB_SUCCESS != result) {
      readMeshIface->report_error("%s: Trouble putting entities in set.\n", fileName);
      return result;
    }

      // add the new set to read_ents
    read_ents.insert(this_set);
  }
    
  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::create_tags	(	ScdInterface *	scdi,
		EntityHandle	file_set,
		const std::vector< int > &	tstep_nums
	)		`[private]`

Definition at line 412 of file ReadGCRM.cpp.

                                                                                                           {
  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);
  ERRORR(rval, "Trouble creating __NUM_DIMS tag.");
  rval = mbImpl->tag_set_data(numDimsTag, &file_set, 1, &numDims);
  ERRORR(rval, "Trouble setting data for __NUM_DIMS tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\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);
  ERRORR(rval, "Trouble creating __NUM_VARS tag.");
  rval = mbImpl->tag_set_data(numVarsTag, &file_set, 1, &numVars);
  ERRORR(rval, "Trouble setting data for __NUM_VARS tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\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);
  ERRORR(rval, "Trouble creating __DIM_NAMES tag.");
  const void* ptr = dimnames.c_str();
  rval = mbImpl->tag_set_by_ptr(dimNamesTag, &file_set, 1, &ptr, &dimnamesSz);
  ERRORR(rval, "Trouble setting data for __DIM_NAMES tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());

  // <__VAR_NAMES>
  Tag varNamesTag = 0;
  tag_name = "__VAR_NAMES";
  std::string varnames;
  std::map<std::string, 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);
  ERRORR(rval, "Trouble creating __VAR_NAMES tag.");
  ptr = varnames.c_str();
  rval = mbImpl->tag_set_by_ptr(varNamesTag, &file_set, 1, &ptr, &varnamesSz);
  ERRORR(rval, "Trouble setting data for __VAR_NAMES tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());

  // __<dim_name>_LOC_MINMAX
  for (unsigned int i = 0; i != dimNamesSz; ++i) {
    if (dimNames[i] == "time") {
      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] = tMin;
      val[1] = tMax;
      rval = mbImpl->tag_get_handle(tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT);
      ERRORR(rval, "Trouble creating __<dim_name>_LOC_MINMAX tag.");
      rval = mbImpl->tag_set_data(tagh, &file_set, 1, &val[0]);
      ERRORR(rval, "Trouble setting data for __<dim_name>_LOC_MINMAX tag.");
      if (MB_SUCCESS == rval)
        dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());
    }
  }

  // __<dim_name>_LOC_VALS
  for (unsigned int i = 0; i != dimNamesSz; ++i) {
    if (dimNames[i] != "time")
      continue;
    std::vector<int> val;
    if (!tstep_nums.empty())
      val = tstep_nums;
    else {
      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);
    ERRORR(rval, "Trouble creating __<dim_name>_LOC_VALS tag.");
    rval = mbImpl->tag_set_data(tagh, &file_set, 1, &val[0]);
    ERRORR(rval, "Trouble setting data for __<dim_name>_LOC_VALS tag.");
    if (MB_SUCCESS == rval)
      dbgOut.tprintf(2, "Tag created for variable %s\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;
    varInfo[mapIter->first].varTags.resize(varDimSz, 0);
    for (unsigned int i = 0; i != varDimSz; ++i) {
      Tag tmptag = 0;
      std::string tmptagname = dimNames[varInfo[mapIter->first].varDims[i]];
      mbImpl->tag_get_handle(tmptagname.c_str(), 0, MB_TYPE_OPAQUE, tmptag, MB_TAG_ANY);
      varInfo[mapIter->first].varTags[i] = tmptag;
    }
    rval = mbImpl->tag_get_handle(tag_name.c_str(), varDimSz, MB_TYPE_HANDLE, varNamesDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT);
    ERRORR(rval, "Trouble creating __<var_name>_DIMS tag.");
    rval = mbImpl->tag_set_data(varNamesDimsTag, &file_set, 1, &(varInfo[mapIter->first].varTags[0]));
    ERRORR(rval, "Trouble setting data for __<var_name>_DIMS tag.");
    if (MB_SUCCESS == rval)
      dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());
  }

  // <PARTITION_METHOD>
  Tag part_tag = scdi->part_method_tag();
  if (!part_tag)
    ERRORR(MB_FAILURE, "Trouble getting partition method tag.");
  rval = mbImpl->tag_set_data(part_tag, &file_set, 1, &partMethod);
  ERRORR(rval, "Trouble setting data for PARTITION_METHOD tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\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);
  ERRORR(rval, "Trouble creating __GLOBAL_ATTRIBS tag.");
  std::string gattVal;
  std::vector<int> gattLen;
  rval = create_attrib_string(globalAtts, gattVal, gattLen);
  ERRORR(rval, "Trouble creating attribute strings.");
  const void* gattptr = gattVal.c_str();
  int globalAttSz = gattVal.size();
  rval = mbImpl->tag_set_by_ptr(globalAttTag, &file_set, 1, &gattptr, &globalAttSz);
  ERRORR(rval, "Trouble setting data for __GLOBAL_ATTRIBS tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\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);
  ERRORR(rval, "Trouble creating __GLOBAL_ATTRIBS_LEN tag.");
  rval = mbImpl->tag_set_data(globalAttLenTag, &file_set, 1, &gattLen[0]);
  ERRORR(rval, "Trouble setting data for __GLOBAL_ATTRIBS_LEN tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\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);
    ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS tag.");
    std::string varAttVal;
    std::vector<int> varAttLen;
    rval = create_attrib_string(mapIter->second.varAtts, varAttVal, varAttLen);
    ERRORR(rval, "Trouble creating attribute strings.");
    const void* varAttPtr = varAttVal.c_str();
    int varAttSz = varAttVal.size();
    rval = mbImpl->tag_set_by_ptr(varAttTag, &file_set, 1, &varAttPtr, &varAttSz);
    ERRORR(rval, "Trouble setting data for __<var_name>_ATTRIBS tag.");
    if (MB_SUCCESS == rval)
      dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());
    if (varAttLen.size() == 0)
      varAttLen.push_back(0);
    ssTagName << "_LEN";
    tag_name = ssTagName.str();
    Tag varAttLenTag = 0;
    rval = mbImpl->tag_get_handle(tag_name.c_str(), varAttLen.size(), MB_TYPE_INTEGER, varAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT);
    ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS_LEN tag.");
    rval = mbImpl->tag_set_data(varAttLenTag, &file_set, 1, &varAttLen[0]);
    ERRORR(rval, "Trouble setting data for __<var_name>_ATTRIBS_LEN tag.");
    if (MB_SUCCESS == rval)
      dbgOut.tprintf(2, "Tag created for variable %s\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);
  ERRORR(rval, "Trouble creating __VAR_NAMES_LOCATIONS tag.");
  for (mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter) {
    varNamesLocs[std::distance(varInfo.begin(), mapIter)] = mapIter->second.entLoc;
  }
  rval = mbImpl->tag_set_data(varNamesLocsTag, &file_set, 1, &varNamesLocs[0]);
  ERRORR(rval, "Trouble setting data for __VAR_NAMES_LOCATIONS tag.");
  if (MB_SUCCESS == rval)
    dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str());

  return MB_SUCCESS;
}

ReaderIface * moab::ReadGCRM::factory ( Interface * iface ) [static]

factory method

Definition at line 29 of file ReadGCRM.cpp.

                                               {
  return new ReadGCRM(iface);
}

ErrorCode moab::ReadGCRM::get_attributes	(	int	var_id,
		int	num_atts,
		std::map< std::string, AttData > &	atts,
		const char *	prefix = `""`
	)		`[private]`

get all global attributes in the file

Definition at line 295 of file ReadGCRM.cpp.

                                                                                                                 {

  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);
    ERRORS(success, "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);
    ERRORS(success, "Trouble getting attribute info.");
    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 moab::ReadGCRM::get_dimensions	(	int	file_id,
		std::vector< std::string > &	dim_names,
		std::vector< int > &	dim_vals
	)		`[private]`

get all dimensions in the file

Definition at line 317 of file ReadGCRM.cpp.

                                                                                                         {
  // get the number of dimensions
  int num_dims;
  int success = NCFUNC(inq_ndims)(file_id, &num_dims);
  ERRORS(success, "Trouble getting number of dimensions.");

  if (num_dims > NC_MAX_DIMS) {
    readMeshIface->report_error("ReadGCRM: File contains %d dims but NetCDF library supports only %d\n", num_dims, (int) NC_MAX_DIMS);
    return MB_FAILURE;
  }

  char dim_name[NC_MAX_NAME + 1];
  NCDF_SIZE dum_len;
  dim_names.resize(num_dims);
  dim_vals.resize(num_dims);

  for (int i = 0; i < num_dims; i++) {
    success = NCFUNC(inq_dim)(file_id, i, dim_name, &dum_len);
    ERRORS(success, "Trouble getting dimension info.");

    dim_vals[i] = dum_len;
    dim_names[i] = std::string(dim_name);

    dbgOut.tprintf(2, "Dimension %s, length=%u\n", dim_name, (unsigned int) dum_len);
  }

  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::get_tag	(	VarData &	var_data,
		int	tstep_num,
		Tag &	tagh,
		int	num_lev
	)		`[private]`

ErrorCode moab::ReadGCRM::get_variables ( ) [private]

get the variable names and other info defined for this file

Definition at line 346 of file ReadGCRM.cpp.

                                  {
  // 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 = dimVals[vit - dimNames.begin()];
  if (!ntimes)
    ntimes = 1;

  // get the number of variables
  int num_vars;
  int success = NCFUNC(inq_nvars)(fileId, &num_vars);
  ERRORS(success, "Trouble getting number of variables.");

  if (num_vars > NC_MAX_VARS) {
    readMeshIface->report_error("ReadGCRM: File contains %d vars but NetCDF library supports only %d\n", num_vars, (int) NC_MAX_VARS);
    return MB_FAILURE;
  }

  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);
    ERRORS(success, "Trouble getting var 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);
    ERRORS(success, "Trouble getting variable data type.");

    // get the number of dimensions, then the dimensions
    success = NCFUNC(inq_varndims)(fileId, i, &var_ndims);
    ERRORS(success, "Trouble getting number of dims of a variable.");
    data.varDims.resize(var_ndims);

    success = NCFUNC(inq_vardimid)(fileId, i, &data.varDims[0]);
    ERRORS(success, "Trouble getting variable dimensions.");

    // finally, get the number of attributes, then the attributes
    success = NCFUNC(inq_varnatts)(fileId, i, &data.numAtts);
    ERRORS(success, "Trouble getting number of dims of a variable.");

    // 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, "   ");
    ERRORR(rval, "Trouble getting attributes for a variable.");

  }

  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::load_file	(	const char *	file_name,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const SubsetList *	subset_list = `0`,
		const Tag *	file_id_tag = `0`
	)		`[virtual]`

Load mesh from a file.

Method all readers must provide to import a mesh.

Parameters:

file_name	The file to read.
file_set	Optional pointer to entity set representing file. If this is not NULL, reader may optionally tag the pointed-to set with format-specific meta-data.
subset_list	An optional struct pointer specifying the tags identifying entity sets to be read.
file_id_tag	If specified, reader should store for each entity it reads, a unique integer ID for this tag.

Author:: Jason Kraftcheck

Implements moab::ReaderIface.

Definition at line 75 of file ReadGCRM.cpp.

{
    // guarantee failure for now
  return MB_FAILURE;
 
  /* VSM: Temporarily commenting out all the relevant code until the above guaranteed failure is fixed */
  /*  
  if (subset_list) {
      // see src/moab/ReaderIface.hpp, definition of SubsetList struct; this basically specifies
      // an integer tag and tag values for sets to read on this proc, or a part number and total # parts
      // for reading a trivial partition of entities
  }

    // save filename to member variable so we don't need to pass as an argument
    // to called functions
  fileName = file_name;

    // process options; see src/FileOptions.hpp for API for FileOptions class, and doc/metadata_info.doc for
    // a description of various options used by some of the readers in MOAB
  ErrorCode result = process_options(opts);
  if (MB_SUCCESS != result) {
    readMeshIface->report_error( "%s: problem reading options\n", fileName);
    return result;
  }

    // Open file; filePtr is member of ReadGCRM, change to whatever mechanism is used to identify file
  FILE* filePtr = fopen( fileName, "r" );
  if (!filePtr)
  {
    readMeshIface->report_error( "%s: fopen returned error.\n", fileName);
    return MB_FILE_DOES_NOT_EXIST;
  }
  
    // read number of verts, elements, sets
  long num_verts = 0, num_elems = 0, num_sets = 0;

    // read_ents keeps a running set of entities read from this file, including vertices, elements, and sets;
    // these will get added to file_set (if input) at the end of the read
  Range read_ents;
  
    // start_vertex is passed back so we know how to convert indices from the file into vertex handles; most
    // of the time this is done by adding start_vertex to the (0-based) index; if the index is 1-based, you also
    // need to subtract one; see read_elements for details
  EntityHandle start_vertex;
  result = read_vertices(num_verts, start_vertex, read_ents);
  if (MB_SUCCESS != result) return result;

    // create/read elements; this template assumes that all elements are the same type, so can be read in a single
    // call to read_elements, and kept track of with a single start_elem handle.  If there are more entity types,
    // might have to keep these start handles in an array/vector.  start_elem is only really needed if you're reading
    // sets later, and need to convert some file-based index to an entity handle
  EntityHandle start_elem;
  result = read_elements(num_elems, start_vertex, start_elem, read_ents);
  if (MB_SUCCESS != result) return result;

    // read/create entity sets; typically these sets have some tag identifying what they're for, see doc/metadata_info.doc
    // for examples of different kinds of sets and how they're marked
  result = create_sets(num_sets, start_vertex, num_verts, start_elem, num_elems, read_ents);
  if (MB_SUCCESS != result) return result;

    // finally, add all read_ents into the file set, if one was input
  if (file_set && *file_set) {
    result = mbImpl->add_entities(*file_set, read_ents);
    if (MB_SUCCESS != result) return result;
  }
  
  return result;
  */
}

unsigned int moab::ReadGCRM::number_dimensions ( ) [inline, private]

number of dimensions in this nc file

Definition at line 261 of file ReadGCRM.hpp.

{
  return dimVals.size();
}

ErrorCode moab::ReadGCRM::process_options ( const FileOptions & opts ) [private]

Process options passed into the reader.

Parameters:

opts	Options passed into this read

Definition at line 258 of file ReadGCRM.cpp.

{
    // mark all options seen, to avoid compile warning on unused variable
  opts.mark_all_seen();
  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::read_elements	(	int	num_elems,
		EntityHandle	start_vertex,
		EntityHandle &	start_elem,
		Range &	read_ents
	)		`[private]`

Read element data and create elements in MOAB database.

read/create elements

Parameters:

num_elems	Number of elements to be read
start_vertex	Starting vertex handle; used to offset connectivity indices
start_elem	Starting element handle; may be used later to offset set entities
read_ents	Range storing all entities read from this file

Definition at line 177 of file ReadGCRM.cpp.

{
    // get the entity type being read
  EntityType ent_type = MBHEX;

    // get the number of vertices per entity
  int verts_per_elem = 8;
  
    // Create the element sequence; passes back a pointer to the internal storage for connectivity and the
    // starting entity handle
  EntityHandle* conn_array;
  ErrorCode result = readMeshIface->get_element_connect( num_elems, verts_per_elem, ent_type,
                                                         1, start_elem, conn_array );
  if (MB_SUCCESS != result) {
    readMeshIface->report_error("%s: Trouble reading elements\n", fileName);
    return result;
  }

    // read connectivity into conn_array directly
  for (long i = 0; i < num_elems; i++) {
      // read connectivity
  }

    // convert file-based connectivity indices to vertex handles in-place; be careful, if indices are smaller than handles,
    // need to do from the end of the list so we don't overwrite data
    //
    // here, we assume indices are smaller than handles, just for demonstration; create an integer-type pointer to connectivity
    // initialized to same start of connectivity array
  int *ind_array = reinterpret_cast<int*>(conn_array);
    // OFFSET is value of first vertex index in file; most files are 1-based, but some might be 0-based
  int OFFSET = 1;
  for (long i = num_elems*verts_per_elem-1; i >= 0; i--) {
    conn_array[i] = ind_array[i] + start_vertex + OFFSET;

      // this assert assumes last handle in read_ents is highest vertex handle in this file
    assert(conn_array[i] >= start_vertex && conn_array[i] <= *read_ents.rbegin());
  }
  
    // notify MOAB of the new elements
  result = readMeshIface->update_adjacencies(start_elem, num_elems, verts_per_elem, conn_array);
  if (MB_SUCCESS != result) return result;

    // add elements to read_ents
  if (num_elems) read_ents.insert(start_elem, start_elem+num_elems-1);
  
  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::read_header ( ) [private]

read the header information

Definition at line 265 of file ReadGCRM.cpp.

                                {
  CPU_WORD_SIZE = sizeof(double);
  IO_WORD_SIZE = sizeof(double);

  dbgOut.tprint(1, "Reading header...\n");

  // get the global attributes
  int numgatts;
  int success;
  success = NCFUNC(inq_natts )(fileId, &numgatts);
  ERRORS(success, "Couldn't get number of global attributes.");

  // read attributes into globalAtts
  ErrorCode result = get_attributes(NC_GLOBAL, numgatts, globalAtts);
  ERRORR(result, "Getting attributes.");
  dbgOut.tprintf(1, "Read %u attributes\n", (unsigned int) globalAtts.size());

  // read in dimensions into dimVals
  result = get_dimensions(fileId, dimNames, dimVals);
  ERRORR(result, "Getting dimensions.");
  dbgOut.tprintf(1, "Read %u dimensions\n", (unsigned int) dimVals.size());

  // read in variables into varInfo
  result = get_variables();
  ERRORR(result, "Getting variables.");
  dbgOut.tprintf(1, "Read %u variables\n", (unsigned int) varInfo.size());

  return MB_SUCCESS;
}

ErrorCode moab::ReadGCRM::read_tag_values	(	const char *	file_name,
		const char *	tag_name,
		const FileOptions &	opts,
		std::vector< int > &	tag_values_out,
		const SubsetList *	subset_list = `0`
	)		`[virtual]`

Read tag values from a file.

Read the list if all integer tag values from the file for a tag that is a single integer value per entity.

Parameters:

file_name	The file to read.
tag_name	The tag for which to read values
tag_values_out	Output: The list of tag values.
subset_list	An array of tag name and value sets specifying the subset of the file to read. If multiple tags are specified, the sets that match all tags (intersection) should be read.
subset_list_length	The length of the 'subset_list' array.

Implements moab::ReaderIface.

Definition at line 408 of file ReadGCRM.cpp.

                                                                                                                    {
  return MB_FAILURE;
}

ErrorCode moab::ReadGCRM::read_vertices	(	int	num_verts,
		EntityHandle &	start_vertex,
		Range &	read_ents
	)		`[private]`

Read vertex data and create vertices in MOAB database.

Parameters:

num_verts	Number of vertices to be read
start_vertex	Starting vertex handle; used later to offset connectivity indices
read_ents	Range storing all entities read from this file

Definition at line 149 of file ReadGCRM.cpp.

{
    // allocate nodes; these are allocated in one shot, get contiguous handles starting with start_handle,
    // and the reader is passed back double*'s pointing to MOAB's native storage for vertex coordinates
    // for those verts
  std::vector<double*> coord_arrays;
  ErrorCode result = readMeshIface->get_node_coords( 3, num_verts, 1, start_vertex, coord_arrays );
  if (MB_SUCCESS != result) {
    readMeshIface->report_error("%s: Trouble reading vertices\n", fileName);
    return result;
  }

    // fill in vertex coordinate arrays
  double *x = coord_arrays[0], 
         *y = coord_arrays[1],
         *z = coord_arrays[2];
  for(long i = 0; i < num_verts; ++i) {
      // empty statement to avoid compiler warning
    if (x || y || z) {}
      // read x/y/z
  }

  if (num_verts) read_ents.insert(start_vertex, start_vertex + num_verts - 1);
  
  return result;
}

void moab::ReadGCRM::reset ( ) [private]

Definition at line 54 of file ReadGCRM.cpp.

                     {
  CPU_WORD_SIZE = -1;
  IO_WORD_SIZE = -1;
  fileId = -1;
  tMin = tMax = -1;
  numUnLim = -1;
  mCurrentMeshHandle = 0;
  startVertex = startElem = 0;
  mGlobalIdTag = 0;
  max_line_length = -1;
  max_str_length = -1;
  vertexOffset = 0;
  dbgOut = stderr;
  mCurrentMeshHandle = 0;
  vertexOffset = 0;

#ifdef USE_MPI
  myPcomm = NULL;
#endif
}