[netCDF #YLU-405033]: dealing with missing values while writing netCDF in FORTRAN V 3.6.1

Avirup,

> Thanks for answering my questions regarding netCDF. I tried to use
> '_FillValue' using the following codes:
> 
> call check(nf90_put_att(ncid,Varid4,'_FillValue', -9999.00))
> 
> Then I read that netCDF file in fortran and R again. But the output array
> contains missing values as -9999.000. I was expecting them to be NaN. I
> looked at the manual for fortran 90. But didn't find any help regarding to
> this subject. Could you plesae help by answering these question:
> 1. Is there way i fill/declare the missing values with some real number and
> then read them as NaN (as we can do in R)

No, that's not supported directly by the netCDF API.  You can define
the value of a variable's _FillValue attribute to be NaN and it will
be read as NaN.  For example, here's some Fortran-90 code that does
that: 

program filltest
  use netcdf
 ...
  real :: fillval, zero
  zero = 0.0
 ...
  call check( nf90_def_var(ncid, "data", NF90_REAL, dimids, varid) )
 ...
  fillval = zero / zero
  call check( nf90_put_att(ncid, varid, "_FillValue", fillval) )
 ...

Now any data not written or written with the value in fillval can be
read as a NaN.

I've attached a full F90 example program modified from an example that
writes incomplete data, with some fill values.  Running the ncdump on
the result shows the unwritten values as '_', which shows they were
read as NaNs.

--Russ


Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: YLU-405033
Department: Support netCDF
Priority: Normal
Status: Closed

!     This is part of the netCDF package.
!     Copyright 2006 University Corporation for Atmospheric Research/Unidata.
!     See COPYRIGHT file for conditions of use.

!     This is a very simple example which writes a 2D array of
!     sample data. To handle this in netCDF we create two shared
!     dimensions, "x" and "y", and a netCDF variable, called "data".

!     This example demonstrates the netCDF Fortran 90 API. This is part
!     of the netCDF tutorial, which can be found at:
!     http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-tutorial
      
!     Full documentation of the netCDF Fortran 90 API can be found at:
!     http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-f90

!     $Id: filltest.f90,v 1.11 2010/04/06 19:32:08 ed Exp $

program filltest
  use netcdf
  implicit none

  ! This is the name of the data file we will create.
  character (len = *), parameter :: FILE_NAME = "filltest.nc"

  ! We are writing 2D data, a 12 x 6 grid. 
  integer, parameter :: NDIMS = 2
  integer, parameter :: NX = 6, NY = 12

  ! When we create netCDF files, variables and dimensions, we get back
  ! an ID for each one.
  integer :: ncid, varid, dimids(NDIMS)
  integer :: x_dimid, y_dimid
  
  ! This is the data array we will write. It will just be filled with
  ! a progression of integers for this example.
  real, dimension(:,:), allocatable :: data_out

  ! Loop indexes, and error handling.
  integer :: x, y
  real :: fillval, zero
  zero = 0.0

  ! Allocate memory for data.
  allocate(data_out(NY-1, NX-1))

  ! Create some pretend data. If this wasn't an example program, we
  ! would have some real data to write, for example, model output.
  do x = 1, NX-1
     do y = 1, NY-1
        data_out(y, x) = (x - 1) * NY + (y - 1)
     end do
  end do

  ! Always check the return code of every netCDF function call. In
  ! this example program, wrapping netCDF calls with "call check()"
  ! makes sure that any return which is not equal to nf90_noerr (0)
  ! will print a netCDF error message and exit.

  ! Create the netCDF file. The nf90_clobber parameter tells netCDF to
  ! overwrite this file, if it already exists.
  call check( nf90_create(FILE_NAME, NF90_CLOBBER, ncid) )

  ! Define the dimensions. NetCDF will hand back an ID for each. 
  call check( nf90_def_dim(ncid, "x", NX, x_dimid) )
  call check( nf90_def_dim(ncid, "y", NY, y_dimid) )

  ! The dimids array is used to pass the IDs of the dimensions of
  ! the variables. Note that in fortran arrays are stored in
  ! column-major format.
  dimids =  (/ y_dimid, x_dimid /)

  ! Define the variable. The type of the variable in this case is
  ! NF90_INT (4-byte integer).
  call check( nf90_def_var(ncid, "data", NF90_REAL, dimids, varid) )

  fillval = zero/ zero
  call check( nf90_put_att(ncid, varid, "_FillValue", fillval) )

  ! End define mode. This tells netCDF we are done defining metadata.
  call check( nf90_enddef(ncid) )

  ! Write the pretend data to the file. Although netCDF supports
  ! reading and writing subsets of data, in this case we write all the
  ! data in one operation.
  call check( nf90_put_var(ncid, varid, data_out) )

  ! Close the file. This frees up any internal netCDF resources
  ! associated with the file, and flushes any buffers.
  call check( nf90_close(ncid) )

  print *, "*** SUCCESS writing example ", FILE_NAME

contains
  subroutine check(status)
    integer, intent ( in) :: status
    
    if(status /= nf90_noerr) then 
      print *, trim(nf90_strerror(status))
      stop 2
    end if
  end subroutine check  
end program filltest