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Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
Hi,
As someone else suggested, the NetCDF operators are very useful. Another useful
way of modifying files is like this:
ncdump file.nc | awkscript.awk | ncgen -o newfile.nc
Where awkscript.awk manipulates the file in the way you want. To illustrate the
point, I am attaching a little script I have been writing to make non-CF
compliant files CF compliant. Maybe this will give you some ideas about how you
can solve your problem?
Cheers,
Tim Hume
Centre for Australian Weather and Climate Research
Melbourne
Australia
---- Example script illustrating use of ncdump, awk and ncgen ----
ncdump "${ncfile}" | awk -F= -v var_name="${var_name}" \
'BEGIN{
nlons = 0;
nlats = 0;
nprogs = 0;
}
/^dimensions:/{
print $0;
printf("\tbounds = 2 ;\n");
prev_line = "dimensions";
next;
}
/^\/\/ global attributes:/{
if ((var_name == "accum_precip")||(var_name ==
"temperature_2m")||(var_name == "dewpoint_2m")){
printf("\tdouble level ;\n");
printf("\t\tlevel:long_name = \"Height above the
surface\" ;\n");
printf("\t\tlevel:units = \"m\" ;\n");
}
print $0;
next;
}
/^data:/{
print $0;
if (var_name == "accum_precip"){
printf("\n level = 0. ;\n");
} else if ((var_name == "temperature_2m")||(var_name ==
"dewpoint_2m")){
printf("\n level = 2. ;\n");
}
next;
}
/^[[:space:]]*longitude:/{
print $0;
prev_line = "longitude_var";
next;
}
/^[[:space:]]*latitude:/{
print $0;
prev_line = "latitude_var";
next;
}
/^[[:space:]]*forecast:/{
print $0;
prev_line = "forecast_var";
next;
}
/^ longitude[[:space:]]+=/,/;$/{
print $0;
n = split($NF,lons,/[,;]/);
for (ii=1; ii<n; ++ii){
lon_vals[ii+nlons] = lons[ii];
}
nlons += (n-1);
prev_line = "longitude_data";
next;
}
/^ latitude[[:space:]]+=/,/;$/{
print $0;
n = split($NF,lats,/[,;]/);
for (ii=1; ii<n; ++ii){
lat_vals[ii+nlats] = lats[ii];
}
nlats += (n-1);
prev_line = "latitude_data";
next;
}
/^ forecast[[:space:]]+=/,/;$/{
print $0;
n = split($NF,progs,/[,;]/);
for (ii=1; ii<n; ++ii){
prog_vals[ii+nprogs] = progs[ii];
}
nprogs += (n-1);
prev_line = "forecast_data";
next;
}
{
if (prev_line == "longitude_var"){
printf("\tdouble longitude_bounds(longitude, bounds)
;\n");
printf("\t\tlongitude_bounds:long_name = \"grid cell
longitude boundaries\" ;\n");
printf("\t\tlongitude_bounds:units = \"degrees_east\"
;\n");
printf("\t\tlongitude_bounds:valid_min = -360.d ;\n");
printf("\t\tlongitude_bounds:valid_max = 360.d ;\n");
}
if (prev_line == "latitude_var"){
printf("\tdouble latitude_bounds(latitude, bounds)
;\n");
printf("\t\tlatitude_bounds:long_name = \"grid cell
latitude boundaries\" ;\n");
printf("\t\tlatitude_bounds:units = \"degrees_north\"
;\n");
printf("\t\tlatitude_bounds:valid_min = -90.d ;\n");
printf("\t\tlatitude_bounds:valid_max = 90.d ;\n");
}
if (prev_line == "forecast_var"){
printf("\tdouble forecast_bounds(forecast, bounds)
;\n");
printf("\t\tforecast_bounds:long_name = \"forecast
interval\" ;\n");
printf("\t\tforecast_bounds:units = \"hours\" ;\n");
}
if (prev_line == "longitude_data"){
printf("\n");
printf(" longitude_bounds = ");
lon1 = lon_vals[1] - (lon_vals[2] - lon_vals[1])/2;
lon2 = lon_vals[1] + (lon_vals[2] - lon_vals[1])/2;
printf("%f, %f, ",lon1, lon2);
for (ii=2; ii<nlons; ++ii){
lon1 = lon_vals[ii] - (lon_vals[ii] -
lon_vals[ii-1])/2;
lon2 = lon_vals[ii] + (lon_vals[ii+1] -
lon_vals[ii])/2;
printf("%f, %f, ",lon1, lon2);
}
lon1 = lon_vals[nlons] - (lon_vals[nlons] -
lon_vals[nlons-1])/2;
lon2 = lon_vals[nlons] + (lon_vals[nlons] -
lon_vals[nlons-1])/2;
printf("%f, %f ;\n",lon1, lon2);
}
if (prev_line == "latitude_data"){
printf("\n");
printf(" latitude_bounds = ");
lat1 = lat_vals[1] - (lat_vals[2] - lat_vals[1])/2;
lat2 = lat_vals[1] + (lat_vals[2] - lat_vals[1])/2;
lat1 = (lat1 < -90) ? -90 : lat1;
lat1 = (lat1 > 90) ? 90 : lat1;
lat2 = (lat2 < -90) ? -90 : lat2;
lat2 = (lat2 > 90) ? 90 : lat2;
printf("%f, %f, ",lat1, lat2);
for (ii=2; ii<nlats; ++ii){
lat1 = lat_vals[ii] - (lat_vals[ii] -
lat_vals[ii-1])/2;
lat2 = lat_vals[ii] + (lat_vals[ii+1] -
lat_vals[ii])/2;
lat1 = (lat1 < -90) ? -90 : lat1;
lat1 = (lat1 > 90) ? 90 : lat1;
lat2 = (lat2 < -90) ? -90 : lat2;
lat2 = (lat2 > 90) ? 90 : lat2;
printf("%f, %f, ",lat1, lat2);
}
lat1 = lat_vals[nlats] - (lat_vals[nlats] -
lat_vals[nlats-1])/2;
lat2 = lat_vals[nlats] + (lat_vals[nlats] -
lat_vals[nlats-1])/2;
lat1 = (lat1 < -90) ? -90 : lat1;
lat1 = (lat1 > 90) ? 90 : lat1;
lat2 = (lat2 < -90) ? -90 : lat2;
lat2 = (lat2 > 90) ? 90 : lat2;
printf("%f, %f ;\n",lat1, lat2);
}
if (prev_line == "forecast_data"){
printf("\n");
printf(" forecast_bounds = ");
for (ii=1; ii<nprogs; ++ii){
if (var_name == "accum_precip"){
prog1 = 0;
prog2 = prog_vals[ii];
} else {
prog1 = prog_vals[ii];
prog2 = prog_vals[ii];
}
printf("%f, %f, ",prog1, prog2);
}
if (var_name == "accum_precip"){
prog1 = 0;
prog2 = prog_vals[nprogs];
} else {
prog1 = prog_vals[nprogs];
prog2 = prog_vals[nprogs];
}
printf("%f, %f ;\n",prog1, prog2);
}
print $0;
prev_line = "other";
}' | fmt -s -w 132 | ncgen -o "${ncfile}.new"
#
# Add some extra attributes etc.
#
ncatted -O -h -a bounds,latitude,o,c,"latitude_bounds" \
-a valid_min,latitude,o,d,-90. \
-a valid_max,latitude,o,d,90. \
-a bounds,longitude,o,c,"longitude_bounds" \
-a valid_min,longitude,o,d,-360. \
-a valid_max,longitude,o,d,360. \
-a bounds,forecast,o,c,"forecast_bounds" \
-a calendar,basetime,o,c,"gregorian" \
-a Conventions,global,o,c,"CF-1.3" \
-a history,global,o,c,"File created by the Gridded OCF data ingest
system" \
-a History,global,d,, \
-a institution,global,o,c,"Australian Bureau of Meteorology" \
-a source,global,o,c,"model" \
-a standard_name,${var_name},o,c,"${std_name}" \
-a title,global,o,c,"${model_str} forecasts of ${var_name}; resolution:
${res_str}; source:${source}" \
-a nco_input_file_number,global,d,, \
-a nco_input_file_list,global,d,, \
"${ncfile}.new"
-----Original Message-----
From: netcdfgroup-bounces@xxxxxxxxxxxxxxxx
[mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Blanquita Oviedo
Sent: Wednesday, 26 November 2008 02:56
To: netcdfgroup@xxxxxxxxxxxxxxxx
Subject: [netcdfgroup] Modifying NEtcdf file
Hi,
I am new using netCDF and I don't know anybody in my country, Colombia,
that is currently working with netCDF files.
In order to make the investigation for my master, I need to modify an a
extensive netCDF file (105.000K). I need to modify aprox 120.000 lines of data,
but I don´t know any method to do it.
I try to convert the source netCDF file into text (using ncdump - o), then I
modified it and now I have an ASCII file separated by commas and with
characters in return in each line, as obtained using the command ncdump of the
original file.
For example:
temp =
// temp(0,0,0, 0-54)
277.4813, 276.4155, 275.3335, 274.2372, 273.4386, 273.0315, 272.6246,
272.2128, 271.7205, 271.1262, 270.5313, 269.9269, 269.3189, 268.7285,
268.1587, 267.6162, 267.5617, 268.1147, 268.6765, 269.2408, 269.4946,
269.3569, 269.1975, 269.0216, 268.8656, 268.7551, 268.6632, 268.5788,
269.1266, 270.4707, 271.8028, 273.1227, 273.7098, 273.3803, 273.0515,
272.7239, 272.7801, 273.3181, 273.8549, 274.3895, 274.682, 274.6729,
274.6642, 274.6566, 274.9037, 275.468, 276.0289, 276.5884, 276.3576,
275.124, 273.8793, 272.6223, 271.6534, 271.0549, 270.4564,
// temp(0,0,1, 0-54)
276.8679, 275.8403, 274.7976, 273.7424, 273.0192, 272.7307, 272.4441,
272.1526, 271.7513, 271.2129, 270.6729, 270.1262, 269.5375, 268.9077,
268.2888, 267.6906, 267.6292, 268.238, 268.859, 269.4889, 269.8028,
269.7146, 269.6006, 269.4674, 269.2771, 269.037, 268.8181, 268.608,
269.0854, 270.4286, 271.7578, 273.0732, 273.6958, 273.4539, 273.2136,
272.9739, 272.9522, 273.2037, 273.4539, 273.7034, 273.8842, 273.9784,
274.0724, 274.1676, 274.4979, 275.1201, 275.7378, 276.3535, 276.2311,
275.1737, 274.1059, 273.0276, 272.2213, 271.7681, 271.3176,
I have problems to return it to turn to netCDF format because the command ncgen
does not work to me. I would like to ask you your support in order to advance
and to obtain a netCDF modified file.
Thanks for the support that you can provide to me.
Blanca Elvira Oviedo T.
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