void DumpableNcFile::dumpvars( void )
{
int n;
static const char* types[] =
{"","byte","char","short","long","float","double"};
NcVar* vp;
for(n = 0; vp = get_var(n); n++) {
cout << "\t" << types[vp->type()] << " " << vp->name() ;
if (vp->num_dims() > 0) {
cout << "(";
for (int d = 0; d < vp->num_dims(); d++) {
NcDim* dim = vp->get_dim(d);
cout << dim->name();
if (d < vp->num_dims()-1)
cout << ", ";
}
cout << ")";
}
cout << " ;\n";
// now dump each of this variable's attributes
dumpatts(*vp);
}
}
void DumpableNcFile::dumpdims( void )
{
for (int n=0; n < num_dims(); n++) {
NcDim* dim = get_dim(n);
cout << "\t" << dim->name() << " = " ;
if (dim->is_unlimited())
cout << "UNLIMITED" << " ;\t " << "// " << dim->size() <<
" currently\n";
else
cout << dim->size() << " ;\n";
}
}
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);
}
}
int main(int argc, char** argv)
{
if (!cmdline(argc, argv))
{
printhelp();
return EXIT_FAILURE;
}
NcFile infile(infilename.c_str(), NcFile::ReadOnly);
if (!infile.is_valid())
{
std::cerr << "Error: invalid input file -- '" << infilename << "'" << std::endl;
infile.close();
return EXIT_FAILURE;
}
NcFile outfile(outfilename.c_str(), NcFile::Replace);
if (!outfile.is_valid())
{
std::cerr << "Error: cannot open output file -- '" << outfilename << "'" << std::endl;
outfile.close();
return EXIT_FAILURE;
}
if (varstrings.size() == 0)
{
std::cerr << "Warning: no variables specified" << std::endl;
}
std::vector<NcVar*> invars;
for (std::vector<std::string>::const_iterator it = varstrings.begin();
it != varstrings.end(); ++it)
{
NcVar* var = infile.get_var((*it).c_str());
if (var == NULL)
{
std::cerr << "Error: " << *it << ": no such variable" << std::endl;
infile.close();
outfile.close();
return EXIT_FAILURE;
}
invars.push_back(var);
}
// extract the distinct set of dims
std::map<std::string, NcDim*> indims;
for (std::vector<NcVar*>::const_iterator it = invars.begin();
it != invars.end(); ++it)
{
NcVar* var = *it;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
indims[dim->name()] = dim;
}
}
// add dims to outfile
std::map<std::string, NcDim*> outdims;
for (std::map<std::string, NcDim*>::const_iterator it = indims.begin();
it != indims.end(); ++it)
{
NcDim* dim = (*it).second;
NcDim* outdim = NULL;
if (dim->is_unlimited())
{
outdim = outfile.add_dim(dim->name());
}
else
{
outdim = outfile.add_dim(dim->name(), dim->size());
}
if (outdim != NULL)
{
outdims[outdim->name()] = outdim;
}
}
// create variables
for (std::vector<NcVar*>::const_iterator it = invars.begin();
it != invars.end(); ++it)
{
NcVar* var = *it;
std::vector<const NcDim*> dims(var->num_dims());
for (int i = 0; i < var->num_dims(); ++i)
{
dims[i] = outdims[var->get_dim(i)->name()];
}
NcVar* outvar = outfile.add_var(var->name(), var->type(), var->num_dims(), &dims[0]);
// identify largest dim, if dim (nearly) exceeds main memory, split along that dim
int maxdim = -1;
long maxdimsize = 0;
long totallen = 1;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
if (dim->size() > maxdimsize)
{
maxdim = i;
maxdimsize = dim->size();
}
totallen *= dim->size();
}
// TODO: support other data types
totallen *= sizeof(float);
// TODO: configurable page size
const unsigned long pagesize = 1000000000;
#ifdef __linux__
struct sysinfo info;
sysinfo(&info);
if (pagesize >= info.freeram)
{
std::cerr << "Warning: page size exceeds free memory" << std::endl;
}
#endif
int numpages = 1;
long pagesizedim = var->get_dim(maxdim)->size();
if (totallen < pagesize)
{
}
else
{
long mul = 1;
for (int i = 0; i < var->num_dims(); ++i)
{
if (i != maxdim)
{
NcDim* dim = var->get_dim(i);
mul *= dim->size();
}
}
// TODO: support other data types
mul *= sizeof(float);
pagesizedim = pagesize / mul;
numpages = var->get_dim(maxdim)->size() / pagesizedim;
if (var->get_dim(maxdim)->size() % pagesizedim > 0)
{
++numpages;
}
}
std::vector< std::vector<long> > curvec;
std::vector< std::vector<long> > countsvec;
std::vector<long> lengths;
int pages = numpages > 0 ? numpages : 1;
for (int p = 0; p < pages; ++p)
{
long len = 1;
std::vector<long> cur;
std::vector<long> counts;
for (int i = 0; i < var->num_dims(); ++i)
{
NcDim* dim = var->get_dim(i);
long current = 0;
long count = dim->size();
if (i == maxdim)
{
current = pagesizedim * p;
count = pagesizedim;
if (p == pages -1)
{
if (dim->size() % pagesizedim != 0)
{
count = dim->size() % pagesizedim;
}
}
}
cur.push_back(current);
counts.push_back(count);
len *= count;
}
curvec.push_back(cur);
countsvec.push_back(counts);
lengths.push_back(len);
}
std::vector< std::vector<long> >::const_iterator it1;
std::vector< std::vector<long> >::const_iterator it2;
std::vector<long>::const_iterator it3;
for (it1 = curvec.begin(), it2 = countsvec.begin(), it3 = lengths.begin();
it1 != curvec.end() && it2 != countsvec.end() && it3 != lengths.end(); ++it1, ++it2, ++it3)
{
std::vector<long> cur = *it1;
std::vector<long> counts = *it2;
long len = *it3;
var->set_cur(&cur[0]);
outvar->set_cur(&cur[0]);
switch (outvar->type())
{
case ncByte:
{
ncbyte* barr = new ncbyte[len];
var->get(barr, &counts[0]);
outvar->put(barr, &counts[0]);
delete[] barr;
break;
}
case ncChar:
{
char* carr = new char[len];
var->get(carr, &counts[0]);
outvar->put(carr, &counts[0]);
delete[] carr;
break;
}
case ncShort:
{
short* sarr = new short[len];
var->get(sarr, &counts[0]);
outvar->put(sarr, &counts[0]);
delete[] sarr;
break;
}
case ncInt:
{
long* larr = new long[len];
var->get(larr, &counts[0]);
outvar->put(larr, &counts[0]);
delete[] larr;
break;
}
case ncFloat:
{
float* farr = new float[len];
var->get(farr, &counts[0]);
outvar->put(farr, &counts[0]);
delete[] farr;
break;
}
case ncDouble:
{
double* darr = new double[len];
var->get(darr, &counts[0]);
outvar->put(darr, &counts[0]);
delete[] darr;
break;
}
default:
break;
}
}
}
infile.close();
outfile.close();
return 0;
}
const std::string name( void ) const
{
return( m_dim->name() );
}
eavlNetCDFImporter::eavlNetCDFImporter(const string &filename)
{
file = new NcFile(filename.c_str(), NcFile::ReadOnly);
if (!file->is_valid())
{
THROW(eavlException,"Couldn't open file!\n");
}
if (debugoutput) cerr << "num_dims="<<file->num_dims()<<endl;
if (debugoutput) cerr << "num_vars="<<file->num_vars()<<endl;
if (debugoutput) cerr << "num_atts="<<file->num_atts()<<endl;
for (int i=0; i<file->num_dims(); i++)
{
NcDim *d = file->get_dim(i);
if (debugoutput) cerr << " dim["<<i<<"]: name="<<d->name()<<" size="<<d->size()<<endl;
}
for (int i=0; i<file->num_atts(); i++)
{
NcAtt *a = file->get_att(i);
if (debugoutput) cerr << " att["<<i<<"]: name="<<a->name()<<" numvals="<<a->num_vals()<<endl;
}
bool found_grid = false;
for (int i=0; i<file->num_vars(); i++)
{
NcVar *v = file->get_var(i);
if (debugoutput)
{
cerr << " var["<<i<<"]: name="<<v->name();
cerr << " ndims="<<v->num_dims();
cerr << " dims = ";
for (int j=0; j<v->num_dims(); j++)
{
cerr << v->get_dim(j)->name();
if (j<v->num_dims()-1)
cerr << "*";
}
cerr << endl;
}
// Here's the condition for what we're going to use;
// we only support one mesh for the moment, so we're picking one.
// Also, the netcdf files we have have the time dim size as "1"
if (v->num_dims() == 4 && string(v->get_dim(0)->name())=="time")
{
if (!found_grid)
{
dims.push_back(v->get_dim(1));
dims.push_back(v->get_dim(2));
dims.push_back(v->get_dim(3));
found_grid = true;
vars.push_back(v);
if (debugoutput) cerr << " * using as first real var\n";
}
else
{
if (string(v->get_dim(1)->name()) == dims[0]->name() &&
string(v->get_dim(2)->name()) == dims[1]->name() &&
string(v->get_dim(3)->name()) == dims[2]->name())
{
vars.push_back(v);
if (debugoutput) cerr << " * using as another var; matches the first real one's dims\n";
}
}
}
}
}
