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addfile

Opens a data file that is (or is to be) written in a supported file format.

Prototype

	function addfile (
		file_path [1] : string,  
		status    [1] : string   
	)

	return_val [1] :  file

Arguments

file_path

The full or relative path of the data file to load.

status

Specifies whether the file should be opened as a read only file or as a read-write file.

Description

The addfile function returns a file variable reference to the file specified by the file_path argument. The file_path string must contain the full or relative path of a file with data in a supported format as well as an extension (a suffix consisting of the final characters following the last dot) that indicates the expected format. The extension is required even though it need not be part of the actual filename. The currently supported formats, valid status values, and accepted extensions are:

NetCDF ("r", "w", "c")
".nc", ".cdf", ".netcdf"

GRIB versions 1 and 2 ("r")
".gr", ".gr1", ".grb", ".grib", ".grb1", ".grib1", ".gr2", "grb2", ".grib2"

(GRIB2 support available in versions 4.3.0 or later. )

HDF-4 ("r", "w", "c")
".hdf", ".hd"

HDFEOS ("r")
".hdfeos", "he2", "he4"

HDF5 ("r", "w")
".h5"

(Limited HDF5 support available in versions 6.0.0 or later. )

HDFEOS5 ("r")
".he5"

CCM ("r")
".ccm"

Shapefile ("r")
".shp" (Shapefile), ".mif" (MapInfo), ".gmt" (Generic Mapping Tools), ".rt1" (TIGER)

(Support for Shapefiles and other geospatial vector-data formats is available in versions 5.1.1 or later. Shapefile support may not be available on all systems.)

addfile handles these extensions in a case-insensitive manner: ".grib", ".GRIB", and ".Grib" all indicate a GRIB file.

The status parameter can be either "r" for read-only, "w" for read-write or "c" for create. When "c" is set, assuming the user has permissions to write in the specified directory and the format is writable, the file is created if it does not exist. If it does exist, an error message is printed and the default missing value for files is returned. When "w" is set, if the file exists, is in a writable format, and has permissions allowing read/write access, the file is opened for reading and writing. If any of these conditions fail, an error message is reported and the default file missing value is returned. Similarly, when "r" is set, if the file exists and has permissions allowing read access, the file is opened for reading; otherwise an error message is printed and the default missing value is returned. See the ismissing function on how to detect the returned missing value in a program.

Use addfiles to reference multiple data files.

Important note: Use the setfileoption procedure to set various options for reading and writing these supported formats. For example, this procedure is critical if you need to read/write large variables from/to a NetCDF file, use NetCDF-4 features, or create NetCDF files using the fast and efficient method. See the examples section of the setfileoption documentation for more information.

There are several functions available for querying what's on the file:

  • getvaratts - return a list of global attributes on the file
  • getfiledimsizes - return a list of dimension sizes
  • getfilevaratts - return a list of attributes associated with a given variable on the file
  • getfilevardims - return a list of dimension names associated with a given variable on the file
  • getfilevardimsizes - return a list of dimension sizes associated with a given variable on the file
  • getfilevarnames - return a list of variable names on the file
  • getfilevartypes - return a list of variable types for the given variable(s) on the file

Older GRIB2 backwards incompatibility note: in version 5.2.0, the GRIB2 code tables were extensively revised to bring them up-to-date with the currently documented state of the parameter tables primarily as defined by NCEP. This may cause some backwards incompatibility issues. For more information and a work-around, see the "GRIB2 backwards incompatibility alert" section in the NCL Reference Manual.

See Also

addfiles, setfileoption, getvaratts, getfiledimsizes, getfilevaratts, getfilevardims, getfilevardimsizes, getfilevarnames, getfilevartypes, isfile, isfilepresent, isfilevar, isfilevaratt, isfilevarcoord

Examples

Below are some basic examples for using addfile for reading and writing various supported formats. For more extensive examples, see the File I/O section of the Applications page.

Example 1

Open a netCDF file called "ex01B1_uv300.hs.nc" as read-only and print its contents:

  a = addfile("ex01B1_uv300.hs.nc","r")
  print(a)                      
Example 2

Open a GRIB 2 file called "fh.0000_tl.press_gr.awp218" and print its contents:

  a = addfile("fh.0000_tl.press_gr.awp218.grb","r")
  print(a)                      
Note that the file name itself contains no extension indicating the format, but that the extension ".grb" is added to the file_path argument. Also note, in the case of GRIB, that you do not need to indicate whether the file is GRIB 1 or GRIB 2. NCL treats all the acceptable GRIB extensions as meaning the same thing. The GRIB version is determined internally.

Example 3

In order to write large variables (>2GB) to a NetCDF file, you must use setfileoption to set the the NetCDF Format option to LargeFile or NetCDF4Classic before you open the file for creation:

   setfileoption("nc","Format","LargeFile")
   f = addfile("my_large_file.nc","c")
or
   setfileoption("nc","Format","NetCDF4Classic")
   f = addfile("my_large_file.nc","c")

It might be asked "Why cannot NCL set this option internally when asked to write a big variable." The answer is that the NetCDF library requires that this decision must be made when the file is first created, before there is any knowledge of the size of variables that will be written. It is possible that eventually the largefile format will be the default NetCDF format, but so far the recommendation from Unidata is to maintain backwards compatibility where possible for applications that can only deal with the original small file format of NetCDF.

Example 4

Here's an example that shows how to access a file being served by an OPeNDAP server, and to test if your version of NCL has OPeNDAP capability built into it:

begin
;---Path to file served by OPeNDAP server at NOAA
  url      = "http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/pressure/"
  filename = "air.1948.nc"

  exists = isfilepresent(url+filename)
  if(.not.exists) then
    print("OPeNDAP test unsuccessful.")
    print("Either the file doesn't exist, or NCL does")
    print("not have OPeNDAP cabilities on this system.")
  else
    f = addfile(url + filename,"r")
    vnames = getfilevarnames(f)
    print(vnames)     ; should be (/"air","time","lon","lat","level"/)
  end if
end 

Example 5

Change values and meta data of a variable using the "w" status option.

  a = addfile("foo.nc","w")

  t = a->TEMP               ; degC
  t = t + 273.15            ; change values
  t@units = "degK"          ; update appropriate attribute

  a->TEMP = t               ; overwrite
Example 6

addfile can modify a variable in a netCDF file, and/or add new variables to it. The script below reads u,v from a file; changes their values; updates the units attribute; creates a new variable (spd) adds attributes; and, finally, writes them out.


  f = addfile("foo.nc","w")

  u = f->U                          ; units  m/s
  v = f->V

  u = 3.2808399 * u                 ; change values (m/s to ft/s)
  v = 3.2808399 * v

  u@units = "ft/s"                  ; update attribute
  v@units = "ft/s"
                                    ; create new variable
  spd = sqrt(u^2 + v^2)

  spd@long_name  = "Wind Speed"
  spd@short_name = "Speed"
  spd@units      = "ft/s"

  f->U = u                          ; write to file (overwrite)
  f->V = v
                                    ; define appropriate information
  filevardef(f, "SPD", typeof(u), getvardims(u))
  f->SPD = spd                      ; write new variable

Example 7

Read in a CCM History Tape (.ccm) and write its contents to a netCDF (.nc) file:

begin
  fname  = "01-11"                       ; file name
  ccmf   = addfile(fname+".ccm","r")     ; open CCM for reading
  system ("rm "+fname+".nc")             ; remove any pre-existing file
  ncdf   = addfile(fname+".nc","c")      ; create new netCDF file

  att_names = getvaratts(ccmf)           ; get CCM file's global attributes
  if(.not.all(ismissing(att_names))) then
    do i = 0,dimsizes(att_names)-1
      print("copy_fileatts: global attributes->" + att_names(i))
      ncdf@$att_names(i)$ = ccmf@$att_names(i)$     ; copy CCM file's global attributes
    end do
  end if
 
  names = getfilevarnames(ccmf)       ; get CCM file's variable names and print them
  print (names)
;
; loop over variables and copy to netCDF file
;
  do i=0, dimsizes(names)-1
    print("writing ncdf: i,name="+ i+ "   "+ names(i))
    ncdf->$names(i)$ = ccmf->$names(i)$
  end do

  print (ncdf)      ; print overview of contents of netCDF file
end