NetCDF 3 Writing

From Wikipedia, the free encyclopedia:

"NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidata program at the University Corporation for Atmospheric Research (UCAR). They are also the chief source of netCDF software, standards development, updates, etc. The format is an open standard. NetCDF Classic and 64-bit Offset Format are an international standard of the Open Geospatial Consortium.

The project is actively supported by UCAR. Version 4.0 (released in 2008) allows the use of the HDF5 data file format. Version 4.1 (2010) adds support for C and Fortran client access to specified subsets of remote data via OPeNDAP.

The format was originally based on the conceptual model of the Common Data Format developed by NASA, but has since diverged and is not compatible with it."

This version of MDArray implements NetCDF-3 file support only. NetCDF-4 is not yet supported.

require 'mdarray'

class NetCDF

  attr_reader :dir, :filename, :max_strlen

#---------------------------------------------------------------------------------------
#
#---------------------------------------------------------------------------------------

def initialize
  @dir = "~/tmp"
  @filename1 = "testWriter"
  @filename2 = "testWriteRecord2"
  @max_strlen = 80
end

#---------------------------------------------------------------------------------------
# Define the NetCDF-3 file
#---------------------------------------------------------------------------------------

def define_file
  
  # We pass the directory, filename, filetype and optionaly the outside_scope.  
  #
  # I'm implementing in cygwin, so the need for method cygpath that converts the 
  # directory name to a Windows name.  In another environment, just pass the directory
  # name.
  # 
  # Inside a block we have another scope, so the block cannot access any variables, etc. 
  # from the ouside scope. If we pass the outside scope, in this case we are passing self,
  # we can access variables in the outside scope by using @outside_scope.<variable>.
  NetCDF.define(cygpath(@dir), @filename1, "netcdf3", self) do
  
    # add dimensions
    dimension "lat", 64
    dimension "lon", 128
  
    # add variables and attributes
    # add Variable double temperature(lat, lon)
    variable "temperature", "double", [@dim_lat, @dim_lon]
    variable_att @var_temperature, "units", "K"
    variable_att @var_temperature, "scale", [1, 2, 3]
  
    # add a string-value variable: char svar(80)
    # note that this is created as a scalar variable although in NetCDF-3 there is no
    # string type and the string has to be represented as a char type.
    variable "svar", "string", [], {:max_strlen => @outside_scope.max_strlen}
  
    # add a 2D string-valued variable: char names(names, 80)
    dimension "names", 3
    variable "names", "string", [@dim_names], {:max_strlen => @outside_scope.max_strlen}
  
    # add a scalar variable
    variable "scalar", "double", []
  
    # add global attributes
    global_att "yo", "face"
    global_att "versionD", 1.2, "double"
    global_att "versionF", 1.2, "float"
    global_att "versionI", 1, "int"
    global_att "versionS", 2, "short"
    global_att "versionB", 3, "byte"
  
  end

end

#---------------------------------------------------------------------------------------
# write data on the above define file
#---------------------------------------------------------------------------------------

def write_file

  NetCDF.write(cygpath(@dir), @filename1, self) do

    temperature = find_variable("temperature")
    shape = temperature.shape
    data = MDArray.fromfunction("double", shape) do |i, j|
      i * 1_000_000 + j * 1_000
    end
    write(temperature, data)

    svar = find_variable("svar")
    write_string(svar, "Two pairs of ladies stockings!")

    names = find_variable("names")
    # careful here with the shape of a string variable.  A string variable has one
    # more dimension than it should as there is no string type in NetCDF-3.  As such,
    # if we look as names' shape it has 2 dimensions, be we need to create a one
    # dimension string array.
    data = MDArray.string([3], ["No pairs of ladies stockings!",
                                "One pair of ladies stockings!",
                                "Two pairs of ladies stockings!"])
    write_string(names, data)

    # write scalar data
    scalar = find_variable("scalar")
    write(scalar, 222.333 )

  end

end

#---------------------------------------------------------------------------------------
# Define a file for writing one record at a time
#---------------------------------------------------------------------------------------

def define_one_at_time

  NetCDF.define(cygpath(@dir), @filename2, "netcdf3", self) do
  
    dimension "lat", 3
    dimension "lon", 4
    # zero sized dimension is an unlimited dimension
    dimension "time", 0
  
    variable "lat", "float", [@dim_lat]
    variable_att @var_lat, "units", "degree_north"

    variable "lon", "float", [@dim_lon]
    variable_att @var_lon, "units", "degree_east"

    variable "rh", "int", [@dim_time, @dim_lat, @dim_lon]
    variable_att @var_rh, "long_name", "relative humidity"
    variable_att @var_rh, "units", "percent"
  
    variable "T", "double", [@dim_time, @dim_lat, @dim_lon]
    variable_att @var_t, "long_name", "surface temperature"
    variable_att @var_t, "units", "degC"

    variable "time", "int", [@dim_time]
    variable_att @var_time, "units", "hours since 1990-01-01"

  end

end

#---------------------------------------------------------------------------------------
# Define a file for writing one record at a time
#---------------------------------------------------------------------------------------

def write_one_at_time

  NetCDF.write(cygpath(@dir), @filename2, self) do

    lat = find_variable("lat")
    lon = find_variable("lon")
    write(lat, MDArray.float([3], [41, 40, 39]))
    write(lon, MDArray.float([4], [-109, -107, -105, -103]))

    # get variables from file
    rh = find_variable("rh")
    time = find_variable("time")
    t = find_variable("T")

    # there is no method find_dimension for NetcdfFileWriter, so we need to get the
    # dimension from a variable.
    rh_shape = rh.shape
    dim_lat = rh_shape[1]
    dim_lon = rh_shape[2]

    (0...10).each do |time_idx|

      # fill rh_data array
      rh_data = MDArray.fromfunction("int", [dim_lat, dim_lon]) do |lat, lon|
        time_idx * lat * lon
      end
      # reshape rh_data so that it has the same shape as rh variable
      # Method reshape! reshapes the array in-place without data copying.
      rh_data.reshape!([1, dim_lat, dim_lon])

      # fill temp_data array
      temp_data = MDArray.fromfunction("double", [dim_lat, dim_lon]) do |lat, lon|
        time_idx * lat * lon / 3.14159
      end
      # reshape temp_data array so that it has the same shape as temp variable.
      temp_data.reshape!([1, dim_lat, dim_lon])
    
      # write the variables
      write(time, MDArray.int([1], [time_idx * 12]), [time_idx])
      write(rh, rh_data, [time_idx, 0, 0])
      write(t, temp_data, [time_idx, 0, 0])

    end # End time_idx loop
  
  end

end

end

netcdf = NetCDF.new
netcdf.define_file
netcdf.write_file
netcdf.define_one_at_time
netcdf.write_one_at_time