Converting 3-dimensional arrays to 2-dimensions
Simple
help netcdf in a MATLAB session and see if it provides you with
information. This software is installed on the University of Washington
Atmospheric Sciences / JISAO computers. The following are quick instructions to
read files and two examples. With luck, you can actually be reading data in 15
minutes. Rene Garreaud provided this script. Contact Todd Mitchell
if you have problems.
1) Let filename.nc be the netCDF file that you want to read.
Type ncdump -h filename.nc in UNIX (not MATLAB) to see
the header of the netCDF file. This will tell you the variable names
and indicate whether or not the variables need to be unpacked when you
read them
into MATLAB. The outputs of this call will be the dimensions and
variables.
Dimensions tells you the variable names and the
dimensions of each variable. For example, lat (short for "latitude") could be a
vector of latitude grid points, and there could be 180 of them for
2-degree latitude resolution global data.
Variables provides information on the variables.
A variable will be introduced asvariable_type variable_name, for example,
float lat. The variable name is then
lat. The scale_factor and
add_offset for the variable, if they are defined, are
used to unpack the data:unpacked_data = ( packed_data * scale_factor ) + add_offset;
2) Type nc = netcdf('filename.nc','nowrite'); in MATLAB to open the netCDF file.
3) The basic command you need in MATLAB is
variable=nc{'variable_name'}(:,:,:,:);
where variable_name is the variable that you
want to read in. The (:,:,:,:)
at the end specifies the dimensions (for example, time,vertical level,lat,lon) that
you want to read in. (:,:,:,:) will read in all of a 4-dimensional
data volume. The order of the arguments is given in the ncdump
output. For NCEP-NCAR reanalysis data provided by CDC, the
vertical level ranges from 1,2,3, ... (don't type in 500 hoping to get 500mb
data). Often the data has been scaled to make for a physically
smaller file. The best example is sea-level pressure (SLP), where a
typical value of 1025.35mb will be written as 2525 in the file. The
scaling information will be included as "add_offset" and
"scale_factor" in the attributes for a variable. Matlab will rescale
the data if you add a "1" to the above command:
variable=nc{'variable_name',1}(:,:,:,:);
Two examples:
Example 1:
ncdump -h sstoi8299.nc
netcdf sstoi8299 {
dimensions:
lat = 180 ;
lon = 360 ;
time = UNLIMITED ; // (216 currently)
variables:
float lat(lat) ;
lat:title = "Latitude" ;
lat:units = "degrees_north" ;
lat:scale_factor = 1.f ;
lat:add_offset = 0.f ;
float lon(lon) ;
lon:title = "Longitude" ;
lon:units = "degrees_east" ;
lon:scale_factor = 1.f ;
lon:add_offset = 0.f ;
double time(time) ;
time:title = "Time" ;
time:units = "days since 1982- 1- 1 0: 0: 0" ;
time:scale_factor = 1.f ;
time:add_offset = 0.f ;
short data(time, lat, lon) ;
data:long_name = "deg.C" ;
data:add_offset = 20.f ;
data:scale_factor = 0.01f ;
data:missing_value = 32767s ;
data:units = "deg.C" ;
nc = netcdf('sstoi8299.nc','nowrite');
ygrid=nc{'lat'}(:);
xgrid=nc{'lon'}(:);
sst=nc{'data',1}(1,:,:);
Reads the latitude and longitude grid points, and the first month
of SST data into MATLAB. The ,1 argument specifies that the SST data
is unpacked using the add_offset and scale_factor information
(see the ncdump output).Example 2:
ncdump -h air.mon.mean.nc
netcdf air.mon.mean {
dimensions:
lon = 144 ;
lat = 73 ;
level = 17 ;
time = UNLIMITED ; // (484 currently)
variables:
...
short air(time, level, lat, lon) ;
That is, we have a global grid of air temperature, with 17 levels
and 484 time samples (monthly from 1958-1997).
The variable air have four dimensions: time, vertical level, lat and lon.
nc = netcdf('air.mon.mean.nc','nowrite');
T=nc{'air'}(21,3,:,:);
whos
Name Size Bytes Class
T 73x144 84096 double array
nc 4-D 1690 netcdf object
The result is in the matlab variable T
Your MATLAB code will need both the MexCDF and MexEPS libraries to run these scripts. I apologize for this inconvenience, but I am a scientist and not a programmer, so I am forced to use everyone elses libraries. Use the following code at your own risk.
The scripts comply with the netCDF standard of the Cooperative Ocean-Atmosphere Research Data Service (COARDS). The metadata information (header) for a simple file written to COARDS specifications is here.
The COARDS standard is for time to be written as "so many units of time since some reference time." Writing and reading time in this way complies with the udunits standard, and keeping track of leap years and historical changes in calendars requires the MexEPS libraries, which are expertly managed by Willa Zhu of NOAA PMEL. The "nc_read.m" script described below will also read files where time is written as "yyyymmddhhmmss" (year, month, day, ...), which is an older in-house convention. The "nc_write.m" script writes the time variable in the COARDS fashion.
Reading a map:
[ data, i4, r4, nam, xgrid, ygrid ] = nc_read( filename, record);
where:
"data" is a vector of the data,
"i4, r4" are vectors containing metadata: number of latitude and longitude points, first latitude point, etc.,
"nam" (optional) variable name
"xgrid, ygrid" (optional) vectors of longitude and latitude points, respectively
"filename" name of file to be read in
"record" number of the record to be read in
The header of the MATLAB script explains these variables in more detail.
nc_read.m -- the MATLAB script.
Writing a map:
nc_write( filename, record, data, nam, i4, r4 );
where
"filename" is the output filename,
"record" is the record number to write,
"data" is a vector containing the data,
"nam" a variable name or units information,
"i4, r4" are vectors containing metadata: number of latitude and longitude points, first latitude point, etc.,
The header of the MATLAB script explains these variables in more detail.
nc_write.m -- the MATLAB script.
Consider A = A(nt,ny,nx) where nt, ny, nx are the number of
time, latitude, and longitude points, respectively.
A = permute( A, [ 3 2 1 ] );
"A" will be dimensioned A(nt,nx*ny), and the second index will first
span the first latitude circle and then the second latitude circle,
and so forth.
A = squeeze( reshape( A, nx*ny,nt,1 ) )' ;
threetotwo.m -- the MATLAB script.