Recipe: Matlab program as OPeNDAP client: Difference between revisions

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Created page with "Back to G5NR Data Access Guide. == Problem == By accessing the collection <code>inst01hr_3d_T_Cv</code> via the OPeNDAP server http://opendap.nccs.nasa.gov/dods/OSSE/G5..."
 
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== Solution ==
== Solution ==
First, we ensure that our NetCDF-4 library has been built with Fortran and OPeNDAP support. If both the queries
MATLAB version 2012a and later has native openDAP support. The following code has been tested with MATLAB version 2014a.
> nc-config --has-f90
> nc-config --has-dap
 
return "yes", we have a compatible NetCDF-4 library. Here <code>nc-config</code> is a utility bundled with NetCDF-4 package.


The metadata for the collection <code>inst01hr_3d_T_Cv</code> is available at
The metadata for the collection <code>inst01hr_3d_T_Cv</code> is available at
Line 23: Line 19:
NOTE:
NOTE:
# Instead of reading a downloaded NetCDF-4 file, we read an OPeNDAP URL.
# Instead of reading a downloaded NetCDF-4 file, we read an OPeNDAP URL.
# While in the downloaded file, the temperature variable appears in the uppercase (T), on the OPeNDAP server, this variable is in lowercase. This is reflected in the call to <code>nf90_inq_varid</code>.
# While in the downloaded file, the temperature variable appears in the uppercase (T), on the OPeNDAP server, this variable is in lowercase.
# Via the OPeNDAP URL, we now have access to all times for which data exists. The hourly <code>inst</code> files are available starting at 2005/15/15, 2200z. Our desired time, 2006/09/18, 0900z is then the 11772<sup>th</sup> step.
# Via the OPeNDAP URL, we now have access to all times for which data exists. The hourly <code>inst</code> files are available starting at 2005/15/15, 2200z. Our desired time, 2006/09/18, 0900z is then the 11772<sup>th</sup> step.


<syntaxhighlight lang="fortran" line>
<syntaxhighlight lang="matlab" line>
program g5nr_reader_dap
% opendap url
 
opdurl = 'http://opendap.nccs.nasa.gov:9090/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv'
  use netcdf          ! for reading the NR files
 
  implicit none
 
  ! File name
  ! ---------
  character(len=256) :: T_file
 
  ! 4D array: (lon,lat,lev,time)
  ! ------------------------------------
  real, allocatable :: T(:,:,:,:)
 
  ! Miscellaneous
  ! -------------
  integer :: ierr
  integer :: im, jm, lm
  integer :: ncid, varid
  integer :: start(4), count(4)
  integer :: imin, imax, jmin, jmax
  real :: minlat, minlon, maxlat, maxlon
 
  ! We replace filename by opendal url
  ! ----------------------------------
  T_file = "http://opendap.nccs.nasa.gov:9090/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv"
 
  ! file name and (subset) dimensions
  ! bounding box:
  !  lons = -130:0.5:-65
  !  lats =  25:0.5:50
  ! ---------------------------------
  ! array indices from the
  ! bounding lat/lon values
  imin = nint((-130. + 180.)/0.5)
  imax = nint(( -65. + 180.)/0.5)
  jmin = nint((  25 +  90.)/0.5)
  jmax = nint((  50 +  90.)/0.5)
  ! array sizes
  im = imax-imin+1
  jm = jmax-jmin+1
  lm = 72
 
  ! Open url and get var id
  ! -----------------------
  call check(nf90_open(T_file,NF90_NOWRITE,ncid), "opening T file")
  call check(nf90_inq_varid(ncid,"t",varid), "getting T varid")
 
  ! Read temperature data
  ! ---------------------
  allocate(T(im,jm,lm,1))            ! global 4D array with 1 time level
  start = [imin, jmin, 1, 11772]    ! time level 11772 corresponds to 2006/09/18, 9z
  count = [im, jm, lm, 1]            ! 1 time level, 3D (lon,lat,lev) array
  write(*,*) 'Reading T...'
  call check(nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
  write(*,*)'T: ', maxval(T),minval(T)
 
  ! close file, release memory
  call check(nf90_close(ncid), "closing T file")
  deallocate(T)
 
  ! All done
  ! --------
 
contains
 
  subroutine check(status, loc)


    integer, intent(in) :: status
% bounding box
    character(len=*), intent(in) :: loc
%  lons = -130:0.5:-65
%  lats =  25:0.5:50
imin = round((-130. + 180.)/0.5);
imax = round(( -65. + 180.)/0.5);
jmin = round((  25 +  90.)/0.5);
jmax = round((  50 +  90.)/0.5);
% corresponding array sizes
im = imax-imin+1;
jm = jmax-jmin+1;
lm = 72; % read all 72 levels


    if(status /= NF90_NOERR) then
% read temperature inside the bounding box
      write (*,*) "Error at ", loc
% time 11772 corresponds to 2006/09/18, 9z
      write (*,*) NF90_STRERROR(status)
start = [imin, jmin, 1, 11772];
    end if
count = [im, jm, lm, 1];
fprintf('Reading Tsub (subset of T)...');
Tsub = ncread(opdurl, 't', start, count);
fprintf('done.\n')


  end subroutine check
% compute max/min of Tsub
fprintf('max(Tsub): %f\n', max(Tsub(:)));
fprintf('min(Tsub): %f\n', min(Tsub(:)));


end program g5nr_reader_dap
% compute max/min of Tsub at surface
level = 72; % surface
Tsub_surface = Tsub(:,:,72);
fprintf('max(Tsub at surface): %f\n', max(Tsub_surface(:)));
fprintf('min(Tsub at surface): %f\n', min(Tsub_surface(:)));
</syntaxhighlight>
</syntaxhighlight>


Revision as of 12:27, 13 November 2014

Back to G5NR Data Access Guide.

Problem

By accessing the collection inst01hr_3d_T_Cv via the OPeNDAP server 

http://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km

we want to read the surface temperature data inside the box bound by latitudes 25oN, 50oN and longitudes -130oW, -65oW for 2006/Sep/18, 9z and compute its min/max.

Solution

MATLAB version 2012a and later has native openDAP support. The following code has been tested with MATLAB version 2014a.

The metadata for the collection inst01hr_3d_T_Cv is available at 

http://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv.info

Code

This code accesses the collection inst01hr_3d_T_Cv from the OPeNDAP server and reads a subset of the temperature data.

NOTE:

  1. Instead of reading a downloaded NetCDF-4 file, we read an OPeNDAP URL.
  2. While in the downloaded file, the temperature variable appears in the uppercase (T), on the OPeNDAP server, this variable is in lowercase.
  3. Via the OPeNDAP URL, we now have access to all times for which data exists. The hourly inst files are available starting at 2005/15/15, 2200z. Our desired time, 2006/09/18, 0900z is then the 11772th step.
% opendap url
opdurl = 'http://opendap.nccs.nasa.gov:9090/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv'

% bounding box
%   lons = -130:0.5:-65
%   lats =   25:0.5:50
imin = round((-130. + 180.)/0.5);
imax = round(( -65. + 180.)/0.5);
jmin = round((  25 +  90.)/0.5);
jmax = round((  50 +  90.)/0.5);
% corresponding array sizes
im = imax-imin+1;
jm = jmax-jmin+1;
lm = 72; % read all 72 levels

% read temperature inside the bounding box
% time 11772 corresponds to 2006/09/18, 9z
start = [imin, jmin, 1, 11772];
count = [im, jm, lm, 1];
fprintf('Reading Tsub (subset of T)...');
Tsub = ncread(opdurl, 't', start, count);
fprintf('done.\n')

% compute max/min of Tsub
fprintf('max(Tsub): %f\n', max(Tsub(:)));
fprintf('min(Tsub): %f\n', min(Tsub(:)));

% compute max/min of Tsub at surface
level = 72; % surface
Tsub_surface = Tsub(:,:,72);
fprintf('max(Tsub at surface): %f\n', max(Tsub_surface(:)));
fprintf('min(Tsub at surface): %f\n', min(Tsub_surface(:)));

Compile and link

We use the utility nf-config (included in the NetCDF-4 installation) to identify the linking rules

For a typical NetCDF-4 installation, the above code, g5nr_reader_dap.f90 can be compiled and linked to the NetCDF-4 library via 

gfortran -o g5nr_reader_dap.x `nf-config --fflags` g5nr_reader_dap.f90 `nf-config --flibs`

creating the executable g5nr_reader_dap.x.

NOTE:

  1. You can use your favorite Fortran compiler instead of gfortran.
  2. If the NetCDF-4 library was built with parallel I/O support, you will need to use mpif90 to link, even if your code does not use the MPI library.

Run

Running the executable, 

./g5nr_reader_dap.x

produces the output 

Reading T (subset)...
T (subset):    305.6048       191.6956

Discussion

See Also

  1. File Spec: File:G5NR-Ganymed-7km FileSpec-ON6-V1.0.pdf
  2. Recipe: Fortran program to read data from downloaded file

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