int netcdf_mpas_read_nvertices ( string filename )
//****************************************************************************80
//
// Purpose:
//
// NETCDF_MPAS_READ_NVERTICES gets the number of vertices.
//
// Licensing:
//
// This code is distributed under the GNU LGPL license.
//
// Modified:
//
// 30 December 2010
//
// Author:
//
// John Burkardt
//
// Reference:
//
// Russ Rew, Glenn Davis, Steve Emmerson, Harvey Davies, Ed Hartne,
// The NETCDF User's Guide,
// Unidata Program Center, March 2009.
//
// Parameters:
//
// Input, string NC_FILENAME, the name of the NETCDF file to examine.
//
// Output, int NETCDF_MPAS_READ_NVERTICES, the value of NVERTICES.
//
{
int nvertices;
long int nvertices_size;
NcDim *nvertices_id;
//
// Open the file.
//
NcFile ncid ( filename.c_str ( ), NcFile::ReadOnly );
//
// Get NCELLS, which is a NETCDF dimension.
//
nvertices_id = ncid.get_dim ( "nVertices" );
nvertices_size = (*nvertices_id).size ( );
//
// Close the file.
//
ncid.close ( );
nvertices = ( int ) nvertices_size;
return nvertices;
}
int netcdf_mpas_read_maxedges ( string filename )
//****************************************************************************80
//
// Purpose:
//
// NETCDF_MPAS_READ_MAXEDGES gets MAXEDGES.
//
// Licensing:
//
// This code is distributed under the GNU LGPL license.
//
// Modified:
//
// 01 January 2011
//
// Author:
//
// John Burkardt
//
// Reference:
//
// Russ Rew, Glenn Davis, Steve Emmerson, Harvey Davies, Ed Hartne,
// The NETCDF User's Guide,
// Unidata Program Center, March 2009.
//
// Parameters:
//
// Input, string NC_FILENAME, the name of the NETCDF file to examine.
//
// Output, int NETCDF_MPAS_READ_MAXEDGES, the value of MAXEDGES.
//
{
int maxedges;
long int maxedges_size;
NcDim *maxedges_id;
//
// Open the file.
//
NcFile ncid ( filename.c_str ( ), NcFile::ReadOnly );
//
// Get MAXEDGES, which is a NETCDF dimension.
//
maxedges_id = ncid.get_dim ( "maxEdges" );
maxedges_size = (*maxedges_id).size ( );
//
// Close the file.
//
ncid.close ( );
maxedges = ( int ) maxedges_size;
return maxedges;
}
bool ReadAstro::open(const char *path)
{
assert(!m_ncfile);
m_ncfile = new NcFile(path, NcFile::ReadOnly);
if (!m_ncfile->is_valid())
{
close();
sendError("failed to open NetCDF file %s", path);
return false;
}
if (m_ncfile->get_format() == NcFile::BadFormat)
{
close();
sendError("bad NetCDF file");
return false;
}
fprintf(stderr, "dims=%d, vars=%d, attrs=%d\n",
m_ncfile->num_dims(), m_ncfile->num_vars(), m_ncfile->num_atts());
for (int i = 0; i < m_ncfile->num_dims(); ++i)
{
fprintf(stderr, "%s: %ld\n",
m_ncfile->get_dim(i)->name(),
m_ncfile->get_dim(i)->size());
}
for (int i = 0; i < m_ncfile->num_vars(); ++i)
{
fprintf(stderr, "%s: dims=%d atts=%d vals=%ld type=%d\n",
m_ncfile->get_var(i)->name(),
m_ncfile->get_var(i)->num_dims(),
m_ncfile->get_var(i)->num_atts(),
m_ncfile->get_var(i)->num_vals(),
m_ncfile->get_var(i)->type());
//int dims = m_ncfile->get_var(i)->num_dims();
NcVar *var = m_ncfile->get_var(i);
for (int j = 0; j < var->num_dims(); ++j)
{
fprintf(stderr, " %s: %ld edge=%ld\n",
var->get_dim(j)->name(),
var->get_dim(j)->size(),
var->edges()[j]);
}
}
for (int i = 0; i < m_ncfile->num_atts(); ++i)
{
fprintf(stderr, "%s\n", m_ncfile->get_att(i)->name());
}
return true;
}
static int load_nc_dim(const NcFile& ncf, const string& name, bool required = true)
{
NcDim* d = 0;
try
{
d = ncf.get_dim(name.c_str());
}
catch(char* str)
{
check(!required, string(str) + "\ndimension " + name + " not found in netcdf file");
}
int size = d ? d->size() : 0;
return size;
}
const bool read( const std::string filename )
{
if ( m_file ) delete m_file;
m_filename = filename;
m_file = new NcFile( filename.c_str(), NcFile::ReadOnly );
if ( !m_file ) return( false );
if ( !m_file->is_valid() ) return( false );
const int ndims = m_file->num_dims();
for ( int i = 0; i < ndims; i++ )
{
m_dims.push_back( new Dim( m_file->get_dim(i) ) );
}
const int nvars = m_file->num_vars();
for ( int i = 0; i < nvars; i++ )
{
m_vars.push_back( new Var( m_file->get_var(i) ) );
}
return( true );
}
void CopyNcVar(
NcFile & ncIn,
NcFile & ncOut,
const std::string & strVarName,
bool fCopyAttributes,
bool fCopyData
) {
if (!ncIn.is_valid()) {
_EXCEPTIONT("Invalid input file specified");
}
if (!ncOut.is_valid()) {
_EXCEPTIONT("Invalid output file specified");
}
NcVar * var = ncIn.get_var(strVarName.c_str());
if (var == NULL) {
_EXCEPTION1("NetCDF file does not contain variable \"%s\"",
strVarName.c_str());
}
NcVar * varOut;
std::vector<NcDim *> dimOut;
dimOut.resize(var->num_dims());
std::vector<long> counts;
counts.resize(var->num_dims());
long nDataSize = 1;
for (int d = 0; d < var->num_dims(); d++) {
NcDim * dimA = var->get_dim(d);
dimOut[d] = ncOut.get_dim(dimA->name());
if (dimOut[d] == NULL) {
if (dimA->is_unlimited()) {
dimOut[d] = ncOut.add_dim(dimA->name());
} else {
dimOut[d] = ncOut.add_dim(dimA->name(), dimA->size());
}
if (dimOut[d] == NULL) {
_EXCEPTION2("Failed to add dimension \"%s\" (%i) to file",
dimA->name(), dimA->size());
}
}
if (dimOut[d]->size() != dimA->size()) {
if (dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (UNLIMITED / %i)",
dimA->name(), dimOut[d]->size());
} else if (!dimA->is_unlimited() && dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / UNLIMITED)",
dimA->name(), dimA->size());
} else if (!dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION3("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / %i)",
dimA->name(), dimA->size(), dimOut[d]->size());
}
}
counts[d] = dimA->size();
nDataSize *= counts[d];
}
// ncByte / ncChar type
if ((var->type() == ncByte) || (var->type() == ncChar)) {
DataVector<char> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
// ncShort type
if (var->type() == ncShort) {
DataVector<short> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt type
if (var->type() == ncInt) {
DataVector<int> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncFloat type
if (var->type() == ncFloat) {
DataVector<float> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncDouble type
if (var->type() == ncDouble) {
DataVector<double> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt64 type
if (var->type() == ncInt64) {
DataVector<ncint64> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// Check output variable exists
if (varOut == NULL) {
_EXCEPTION1("Unable to create output variable \"%s\"",
var->name());
}
// Copy attributes
if (fCopyAttributes) {
CopyNcVarAttributes(var, varOut);
}
}
//
// Reads variable data from dump file
//
bool DataVar::initFromFile(const string& filename, const_DomainChunk_ptr dom)
{
cleanup();
#if ESYS_HAVE_NETCDF
NcError ncerr(NcError::silent_nonfatal);
NcFile* input = new NcFile(filename.c_str());
if (!input->is_valid()) {
cerr << "Could not open input file " << filename << "." << endl;
delete input;
return false;
}
NcDim* dim;
NcAtt* att;
att = input->get_att("type_id");
int typeID = att->as_int(0);
if (typeID != 2) {
cerr << "WARNING: Only expanded data supported!" << endl;
delete input;
return false;
}
att = input->get_att("rank");
rank = att->as_int(0);
dim = input->get_dim("num_data_points_per_sample");
ptsPerSample = dim->size();
att = input->get_att("function_space_type");
funcSpace = att->as_int(0);
centering = dom->getCenteringForFunctionSpace(funcSpace);
dim = input->get_dim("num_samples");
numSamples = dim->size();
#ifdef _DEBUG
cout << varName << ":\t" << numSamples << " samples, "
<< ptsPerSample << " pts/s, rank: " << rank << endl;
#endif
domain = dom;
NodeData_ptr nodes = domain->getMeshForFunctionSpace(funcSpace);
if (nodes == NULL) {
delete input;
return false;
}
meshName = nodes->getName();
siloMeshName = nodes->getFullSiloName();
initialized = true;
size_t dimSize = 1;
vector<long> counts;
if (rank > 0) {
dim = input->get_dim("d0");
int d = dim->size();
shape.push_back(d);
counts.push_back(d);
dimSize *= d;
}
if (rank > 1) {
dim = input->get_dim("d1");
int d = dim->size();
shape.push_back(d);
counts.push_back(d);
dimSize *= d;
}
if (rank > 2) {
cerr << "WARNING: Rank " << rank << " data is not supported!\n";
initialized = false;
}
if (initialized && numSamples > 0) {
sampleID.insert(sampleID.end(), numSamples, 0);
NcVar* var = input->get_var("id");
var->get(&sampleID[0], numSamples);
size_t dataSize = dimSize*numSamples*ptsPerSample;
counts.push_back(ptsPerSample);
counts.push_back(numSamples);
float* tempData = new float[dataSize];
var = input->get_var("data");
var->get(tempData, &counts[0]);
const float* srcPtr = tempData;
for (size_t i=0; i < dimSize; i++, srcPtr++) {
float* c = averageData(srcPtr, dimSize);
dataArray.push_back(c);
}
delete[] tempData;
initialized = reorderSamples();
}
delete input;
#endif // ESYS_HAVE_NETCDF
return initialized;
}
void netcdf_mpas_report ( string filename )
//****************************************************************************80
//
// Purpose:
//
// NETCDF_MPAS_REPORT reads an MPAS NETCDF grid file and reports.
//
// Discussion:
//
// In this example, we want to extract all the information from a file
// of unknown type.
//
// Here, we are pretending we have no idea what's in the file, so we
// have to go step by step, making inquiries to NETCDF.
//
// As we go, we print out what we have discovered. We don't attempt
// to return any of the data.
//
// Licensing:
//
// This code is distributed under the GNU LGPL license.
//
// Modified:
//
// 29 December 2010
//
// Author:
//
// John Burkardt
//
// Reference:
//
// Russ Rew, Glenn Davis, Steve Emmerson, Harvey Davies, Ed Hartne,
// The NETCDF User's Guide,
// Unidata Program Center, March 2009.
//
// Parameters:
//
// Input, string FILENAME, the name of the NETCDF file to examine.
//
{
NcAtt *att;
NcDim *dim;
int i;
int j;
long int len;
NcToken name;
int num_atts;
int num_dims;
int num_vars;
NcType type;
NcDim *unlimdimid;
NcVar *var;
cout << "\n";
cout << "NETCDF_MPAS_REPORT:\n";
cout << " Report the information stored in a NETCDF\n";
cout << " file. Although we wish to examine a file containing\n";
cout << " grid data generated by MPAS, we will assume we do not\n";
cout << " have any idea of what is in the file. So we just read,\n";
cout << " inquire, and print out.\n";
cout << "\n";
cout << " The name of the file is \"" << filename << "\"\n";
//
// Open the file.
//
NcFile ncid ( filename.c_str ( ), NcFile::ReadOnly );
//
// Return information about the NETCDF file.
//
num_dims = ncid.num_dims ( );
num_vars = ncid.num_vars ( );
num_atts = ncid.num_atts ( );
unlimdimid = ncid.rec_dim ( );
cout << "\n";
cout << "PRIMARY PARAMETERS:\n";
cout << "\n";
cout << " The number of dimensions NUM_DIMS = " << num_dims << "\n";
cout << " The number of variables NUM_VARS = " << num_vars << "\n";
cout << " The number of global attributes NUM_ATTS = " << num_atts << "\n";
cout << " The unlimited dimension (if any) UNLIMDIMID = \"" << (*unlimdimid).name ( ) << "\"\n";
//
// Retrieve global attributes.
// First, we must evaluate the constant "NC_GLOBAL".
//
// nc_global = netcdf.getConstant ( 'NC_GLOBAL' );
cout << "\n";
cout << "GLOBAL ATTRIBUTES:\n";
cout << " Att --------Name-------- Type Len\n";
cout << "\n";
for ( i = 0; i < num_atts; i++ )
{
att = ncid.get_att ( i );
name = (*att).name ( );
type = (*att).type ( );
len = (*att).num_vals ( );
cout << " " << setw(2) << i
<< " \"" << setw(18) << name << "\""
<< " " << setw(4) << type
<< " " << setw(4) << len << "\n";
}
//
// Determine names and extents of dimensions.
// Since each NAME is a char array, we make a cell array to hold them.
//
cout << "\n";
cout << "DIMENSIONS:\n";
cout << " Dim --------Name-------- Extent\n";
cout << "\n";
for ( i = 0; i < num_dims; i++ )
{
dim = ncid.get_dim ( i );
name = (*dim).name ( );
len = (*dim).size ( );
cout << " " << setw(2) << i
<< " \"" << setw(18) << name << "\""
<< " " << setw(6) << len << "\n";
}
//
// Get variable names, types, dimensions, number of attributes.
//
cout << "\n";
cout << "VARIABLES:\n";
cout << " Var --------Name-------- Type Natts Ndims Dims\n";
cout << "\n";
for ( i = 0; i < num_vars; i++ )
{
var = ncid.get_var ( i );
name = (*var).name ( );
type = (*var).type ( );
num_dims = (*var).num_dims ( );
num_atts = (*var).num_atts ( );
cout << " " << setw(2) << i
<< " \"" << setw(18) << name << "\""
<< " " << setw(4) << type
<< " " << setw(4) << num_atts
<< " " << setw(4) << num_dims
<< " ";
for ( j = 0; j < num_dims; j++ )
{
dim = (*var).get_dim ( j );
if ( j == 0 )
{
cout << "[";
}
cout << (*dim).name ( );
if ( j < num_dims - 1 )
{
cout <<",";
}
else
{
cout << "]";
}
}
cout << "\n";
}
//
// Close the file.
//
ncid.close ( );
return;
}
void size_read ( string filename, int *dim, int *vertices, int *edges,
int *triangles, int *quadrilaterals, int *tetrahedrons, int *hexahedrons )
//*****************************************************************************80
//
// Purpose:
//
// SIZE_READ reads ICE sizes from a NETCDF file.
//
// Licensing:
//
// This code is distributed under the GNU LGPL license.
//
// Modified:
//
// 30 November 2010
//
// Author:
//
// John Burkardt
//
// Reference:
//
// Pascal Frey,
// MEDIT: An interactive mesh visualization software,
// Technical Report RT-0253,
// Institut National de Recherche en Informatique et en Automatique,
// 03 December 2001.
//
// Parameters:
//
// Input, string FILENAME, the name of the file to be read.
// Ordinarily, the name should include the extension ".nc".
//
// Output, int *DIM, the spatial dimension, which should be 2 or 3.
//
// Output, int *VERTICES, the number of vertices.
//
// Output, int *EDGES, the number of edges (may be 0).
//
// Output, int *TRIANGLES, the number of triangles (may be 0).
//
// Output, int *QUADRILATERALS, the number of quadrilaterals (may be 0).
//
// Output, int *TETRAHEDRONS, the number of tetrahedrons (may be 0).
//
// Output, int *HEXAHEDRONS, the number of hexahedrons (may be 0).
//
{
NcDim *dim_dimension;
NcDim *dim_edges;
NcDim *dim_eight;
NcDim *dim_four;
NcDim *dim_hexahedrons;
NcToken dim_name;
int dim_num;
NcDim *dim_quadrilaterals;
NcDim *dim_tetrahedrons;
NcDim *dim_three;
NcDim *dim_triangles;
NcDim *dim_two;
NcDim *dim_vertices;
NcDim *dim_pointer;
int i;
//
// Initialize everything to nothing.
//
*dim = 0;
*vertices = 0;
*edges = 0;
*triangles = 0;
*quadrilaterals = 0;
*tetrahedrons = 0;
*hexahedrons = 0;
//
// Open the file in "read only" mode.
//
NcFile dataFile ( filename.c_str ( ), NcFile::ReadOnly );
if ( !dataFile.is_valid ( ) )
{
cout << "\n";
cout << "SIZE_READ: Fatal error!\n";
cout << " Could not open file.\n";
exit ( 1 );
}
//
// Get the dimension information.
//
// I would much prefer to write "0" as the size of certain dimensions, but I am not
// allowed to, so I simply omit them from the file.
//
// Therefore, when I open the file and try to determine dimensions, some dimensions
// are "missing", which I would have presumed I could discover painlessly by asking
// for pointers to them, and getting NULLs back. But that doesn't seem to work either.
//
// So my bonehead backup is simply to read all the dimensions by index, retrieve
// their names, and see what I find.
//
dim_num = dataFile.num_dims ( );
for ( i = 0; i < dim_num; i++ )
{
dim_pointer = dataFile.get_dim ( i );
dim_name = dim_pointer->name ( );
if ( !strcmp ( dim_name, "Dimension" ) )
{
*dim = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Vertices" ) )
{
*vertices = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Edges" ) )
{
*edges = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Triangles" ) )
{
*triangles = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Quadrilaterals" ) )
{
*quadrilaterals = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Tetrahedrons" ) )
{
*tetrahedrons = dim_pointer->size ( );
}
else if ( !strcmp ( dim_name, "Hexahedrons" ) )
{
*hexahedrons = dim_pointer->size ( );
}
else
{
cout << " Ignoring information about dimension \"" << dim_name << "\".\n";
}
}
//
// Close the file.
//
dataFile.close ( );
return;
}