Hello netcdf-ers,
I had a user of the R ncdf4 package alert me to an odd and perplexing
apparent bug in the netcdf library. It is triggered by the netcdf file you
can download here:
http://cirrus.ucsd.edu/~pierce/tmp/mendota_buoy.2018-11-08.nc
This file has the following variable (among others):
float phycocyanin(time) ;
phycocyanin:_FillValue = -9999.f ;
phycocyanin:units = "RFU" ;
phycocyanin:long_name = "Phycocyanin" ;
phycocyanin:_Storage = "chunked" ;
phycocyanin:_ChunkSizes = 1440 ;
phycocyanin:_DeflateLevel = 4 ;
phycocyanin:_Shuffle = "true" ;
phycocyanin:_Endianness = "little" ;
'ncdump' reports all the data as missing:
phycocyanin = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
(etc.)
When I read the data into a floating point array using the C library using
nc_get_var_float() then I get the expected values of -9999.0. However when
I read it into a double precision array with nc_get_var_double() then I get
strange values. Here is the output of the little test program that I've
appended below:
Sizeof float: 4 double: 8
======== DOUBLE ========
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
-559239646634519513659653226496.000000
======== FLOAT ========
-9999.000000 -9999.000000 -9999.000000 -9999.000000 -9999.000000
-9999.000000 -9999.000000 -9999.000000 -9999.000000 -9999.000000
This seems like a bug, unless I'm overlooking something obvious in the test
code (always possible). The nc_get_var_double() call is supposed to convert
the netcdf file's values into double precision and store them in the
provided double precision array, right? That's my understanding anyway. I
can't see why they are not -9999.00's in the resultant array.
Any thoughts are appreciated,
--Dave
Test program:
#include <stdio.h>
#include <stdlib.h>
#include "netcdf.h"
void main( int argc, char *argv[] )
{
int err, ncid, varid;
size_t nt;
double *ddat;
float *fdat;
nt = 1440; /* just hardcode for test */
printf( "Sizeof float: %ld double: %ld\n", sizeof(float),
sizeof(double) );
err = nc_open("mendota_buoy.2018-11-08.nc", 0, &ncid );
if( err != 0 ) {
printf( "err open = %d\n", err );
exit(-1);
}
err = nc_inq_varid( ncid, "phycocyanin", &varid );
if( err != 0 ) {
printf( "err inq_varid = %d\n", err );
exit(-1);
}
/* Make room for both double and floating dat */
ddat = (double *)malloc( sizeof(double) * nt );
fdat = (float *)malloc( sizeof(float ) * nt );
/* Read into double array. Supposed to convert to double...? */
err = nc_get_var_double( ncid, varid, ddat );
if( err != 0 ) {
printf( "err get_var_double = %d\n", err );
exit(-1);
}
printf( "======== DOUBLE ========\n" );
for( int ii=0; ii<10; ii++ )
printf( "%lf ", ddat[ii] );
printf( "\n" );
/* === Do same thing, but for float === */
err = nc_get_var_float( ncid, varid, fdat );
if( err != 0 ) {
printf( "err get_var_float = %d\n", err );
exit(-1);
}
printf( "======== FLOAT ========\n" );
for( int ii=0; ii<10; ii++ )
printf( "%f ", fdat[ii] );
printf( "\n" );
}
-------------------------------------------------------------------
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography
(858) 534-8276 (voice) / (858) 534-8561 (fax) dpierce@xxxxxxxx
-------------------------------------------------------------------
