Joe Sirott wrote:
Hi,
Anyone know of a quick way to convert a relatively large (~2GB)
netcdf-3 file with a record dimension to a netcdf-3 file with all
fixed dimensions?
Attached is our program to reorder netCDF files.
Chris
/*
-------------------------------------------------------------------------
OBJECT NAME: ncReorder
ENTRY POINTS: main
STATIC FNS: none
DESCRIPTION: Reorder an existing netCDF file, changing the UNLIMITED
dimension to a fixed dimension. This has the affect of
making all the data for given variable contiguous on disk.
INPUT: netCDF file
OUTPUT: netCDF file
NOTES:
COPYRIGHT: University Corporation for Atmospheric Research, 2004-09
-------------------------------------------------------------------------
*/
#include <netcdf.hh>
#include <cstdio>
#include <cstring>
bool verbose = false;
/* -------------------------------------------------------------------- */
int main(int argc, char *argv[])
{
int argIndx = 1;
if (argc < 3)
{
fprintf(stderr, "Usage: ncReorder [-v] infile.nc outfile.nc\n");
return(1);
}
if (strcmp(argv[argIndx], "-v") == 0)
{
verbose = true;
++argIndx;
}
NcFile inFile(argv[argIndx++]);
if (!inFile.is_valid())
{
fprintf(stderr, "ncReorder: Invalid input file, exiting.\n");
return(1);
}
if (!inFile.get_dim("Time")->is_unlimited())
{
fprintf(stderr,
"ncReorder: 'Time' dimension is not UNLIMITED, reorder
unnecessary...\n");
return(1);
}
NcFile outFile(argv[argIndx++], NcFile::Replace);
outFile.set_fill(NcFile::NoFill);
if (!outFile.is_valid())
{
fprintf(stderr, "ncReorder: Unable to create/destroy output file,
exiting.\n");
return(1);
}
// Transfer dimensions.
for (int i = 0; i < inFile.num_dims(); ++i)
outFile.add_dim(inFile.get_dim(i)->name(), inFile.get_dim(i)->size());
// Transfer global attributes.
for (int i = 0; i < inFile.num_atts(); ++i)
outFile.add_att(inFile.get_att(i)->name(), inFile.get_att(i)->num_vals(),
(const char *)inFile.get_att(i)->values()->base());
// Transfer Variables.
NcVar *var;
NcDim *dims[6];
for (int i = 0; i < inFile.num_vars(); ++i)
{
var = inFile.get_var(i);
//printf("%s\n", var->name());
// Transfer dims for the var.
for (int j = 0; j < var->num_dims(); ++j)
for (int k = 0; k < outFile.num_dims(); ++k)
if (var->get_dim(j)->size() == outFile.get_dim(k)->size())
{
dims[j] = outFile.get_dim(k);
break;
}
outFile.add_var(var->name(), var->type(), var->num_dims(), (const
NcDim**)dims);
// Transfer variable attributes.
for (int j = 0; j < var->num_atts(); ++j)
{
NcAtt *att = var->get_att(j);
switch (att->type())
{
case ncChar:
outFile.get_var(i)->add_att(att->name(), att->num_vals(),
(const char *)att->values()->base());
break;
case ncFloat:
outFile.get_var(i)->add_att(att->name(), att->num_vals(),
(const float *)att->values()->base());
break;
case ncInt:
outFile.get_var(i)->add_att(att->name(), att->num_vals(),
(const long *)att->values()->base());
break;
default:
fprintf(stderr, "Currently unsupported data type in var attr
transfer.\n");
}
}
}
// Transfer data.
long nVars = inFile.num_vars();
for (int i = 0; i < nVars; ++i)
{
if (verbose)
printf("%s , nDims = %d\n", inFile.get_var(i)->name(),
inFile.get_var(i)->num_dims());
else
{
printf("\r%d%%", (int)(100 * ((float)i / nVars)));
fflush(stdout);
}
if (inFile.get_var(i)->num_dims() == 0)
{
int v = inFile.get_var(i)->as_int(0);
long l = 1;
outFile.get_var(i)->put(&v, &l);
}
else
{
long *edges = inFile.get_var(i)->edges();
if (inFile.get_var(i)->type() == ncFloat)
{
float *data = new float[inFile.get_var(i)->num_vals()];
inFile.get_var(i)->get(data, inFile.get_var(i)->edges());
outFile.get_var(i)->put(data, outFile.get_var(i)->edges());
delete [] data;
}
else
if (inFile.get_var(i)->type() == ncInt)
{
int *data = new int[inFile.get_var(i)->num_vals()];
inFile.get_var(i)->get(data, inFile.get_var(i)->edges());
outFile.get_var(i)->put(data, outFile.get_var(i)->edges());
delete [] data;
}
delete [] edges;
}
}
printf("\n");
inFile.close();
outFile.close();
return(0);
}
