source: trunk/anuga_core/source/anuga/file/netcdf.py @ 8780

""" This module is responsible for loading and saving NetCDF NC files
"""

import numpy as num

from anuga.coordinate_transforms.redfearn import \
     convert_from_latlon_to_utm
from anuga.config import minimum_storable_height as \
     default_minimum_storable_height
from anuga.config import netcdf_mode_r, netcdf_mode_w
from anuga.config import netcdf_float, netcdf_int
from anuga.utilities.numerical_tools import ensure_numeric,  mean

import anuga.utilities.log as log


# Definitions of various NetCDF dimension names, etc.
lon_name = 'LON'
lat_name = 'LAT'
time_name = 'TIME'
precision = netcdf_float # So if we want to change the precision its done here



def NetCDFFile(file_name, netcdf_mode=netcdf_mode_r):
    """Wrapper to isolate changes of the netcdf libray.

    In theory we should be able to change over to NetCDF4 via this
    wrapper, by ensuring the interface to the NetCDF library isthe same as the
    the old Scientific.IO.NetCDF library.

    There is a difference between extracting dimensions. We have used the following
    to cover netcdf4 and scientific python

    try: # works with netcdf4
        number_of_timesteps = len(fid.dimensions['number_of_timesteps'])
        number_of_points = len(fid.dimensions['number_of_points'])
    except: # works with scientific.io.netcdf
        number_of_timesteps = fid.dimensions['number_of_timesteps']
        number_of_points = fid.dimensions['number_of_points']
    
    """

    #from Scientific.IO.NetCDF import NetCDFFile
    #return NetCDFFile(file_name, netcdf_mode)

    from netCDF4 import Dataset
    return Dataset(file_name, netcdf_mode, format='NETCDF3_64BIT')

    #return Dataset(file_name, netcdf_mode, format='NETCDF3_CLASSIC')


    # COMMENT SR; Can't use scipy.io.netcdf as we can't append to
    # a file as of 2013/03/26
    #from scipy.io.netcdf import netcdf_file
    #return netcdf_file(file_name, netcdf_mode, version=2)




class Write_nc:
    """Write an nc file.

    Note, this should be checked to meet cdc netcdf conventions for gridded
    data. http://www.cdc.noaa.gov/cdc/conventions/cdc_netcdf_standard.shtml
    """

    def __init__(self,
                 quantity_name,
                 file_name,
                 time_step_count,
                 time_step,
                 lon,
                 lat):
        """Instantiate a Write_nc instance (NetCDF file writer).

        time_step_count is the number of time steps.
        time_step is the time step size

        pre-condition: quantity_name must be 'HA', 'UA'or 'VA'.
        """

        self.quantity_name = quantity_name
        quantity_units = {'HA':'CENTIMETERS',
                          'UA':'CENTIMETERS/SECOND',
                          'VA':'CENTIMETERS/SECOND'}

        multiplier_dic = {'HA':100.0,   # To convert from m to cm
                          'UA':100.0,   #             and m/s to cm/sec
                          'VA':-100.0}  # MUX files have positive x in the
                                        # Southern direction.  This corrects
                                        # for it, when writing nc files.

        self.quantity_multiplier =  multiplier_dic[self.quantity_name]

        #self.file_name = file_name
        self.time_step_count = time_step_count
        self.time_step = time_step

        # NetCDF file definition
        self.outfile = NetCDFFile(file_name, netcdf_mode_w)
        outfile = self.outfile

        #Create new file
        nc_lon_lat_header(outfile, lon, lat)

        # TIME
        outfile.createDimension(time_name, None)
        outfile.createVariable(time_name, precision, (time_name,))

        #QUANTITY
        outfile.createVariable(self.quantity_name, precision,
                               (time_name, lat_name, lon_name))
        outfile.variables[self.quantity_name].missing_value = -1.e+034
        outfile.variables[self.quantity_name].units = \
                                 quantity_units[self.quantity_name]
        outfile.variables[lon_name][:]= ensure_numeric(lon)
        outfile.variables[lat_name][:]= ensure_numeric(lat)

        #Assume no one will be wanting to read this, while we are writing
        #outfile.close()

    def store_timestep(self, quantity_slice):
        """Write a time slice of quantity info

        quantity_slice is the data to be stored at this time step
        """

        # Get the variables
        time = self.outfile.variables[time_name]
        quantity = self.outfile.variables[self.quantity_name]

        # get index oflice to write
        i = len(time)

        #Store time
        time[i] = i * self.time_step    #self.domain.time
        quantity[i,:] = quantity_slice * self.quantity_multiplier

    def close(self):
        """ Close file underlying the class instance. """
        self.outfile.close()



def write_elevation_nc(file_out, lon, lat, depth_vector):
    """Write an nc elevation file."""

    # NetCDF file definition
    outfile = NetCDFFile(file_out, netcdf_mode_w)

    #Create new file
    nc_lon_lat_header(outfile, lon, lat)

    # ELEVATION
    zname = 'ELEVATION'
    outfile.createVariable(zname, precision, (lat_name, lon_name))
    outfile.variables[zname].units = 'CENTIMETERS'
    outfile.variables[zname].missing_value = -1.e+034

    outfile.variables[lon_name][:] = ensure_numeric(lon)
    outfile.variables[lat_name][:] = ensure_numeric(lat)

    depth = num.reshape(depth_vector, (len(lat), len(lon)))
    outfile.variables[zname][:] = depth

    outfile.close()


def nc_lon_lat_header(outfile, lon, lat):
    """Write lat/lon headers to a NetCDF file.

    outfile is the netcdf file handle.
    lon - a list/array of the longitudes
    lat - a list/array of the latitudes
    """

    outfile.institution = 'Geoscience Australia'
    outfile.description = 'Converted from URS binary C'

    # Longitude
    outfile.createDimension(lon_name, len(lon))
    outfile.createVariable(lon_name, precision, (lon_name,))
    outfile.variables[lon_name].point_spacing = 'uneven'
    outfile.variables[lon_name].units = 'degrees_east'
    outfile.variables[lon_name].assignValue(lon)

    # Latitude
    outfile.createDimension(lat_name, len(lat))
    outfile.createVariable(lat_name, precision, (lat_name,))
    outfile.variables[lat_name].point_spacing = 'uneven'
    outfile.variables[lat_name].units = 'degrees_north'
    outfile.variables[lat_name].assignValue(lat)




def filter_netcdf(filename1, filename2, first=0, last=None, step=1):
    """Filter data file, selecting timesteps first:step:last.
    
    Read netcdf filename1, pick timesteps first:step:last and save to
    nettcdf file filename2
    """

    from Scientific.IO.NetCDF import NetCDFFile

    # Get NetCDF
    infile = NetCDFFile(filename1, netcdf_mode_r)  #Open existing file for read
    outfile = NetCDFFile(filename2, netcdf_mode_w)  #Open new file

    # Copy dimensions
    for d in infile.dimensions:
        outfile.createDimension(d, infile.dimensions[d])

    # Copy variable definitions
    for name in infile.variables:
        var = infile.variables[name]
        outfile.createVariable(name, var.dtype.char, var.dimensions)

    # Copy the static variables
    for name in infile.variables:
        if name == 'time' or name == 'stage':
            pass
        else:
            outfile.variables[name][:] = infile.variables[name][:]

    # Copy selected timesteps
    time = infile.variables['time']
    stage = infile.variables['stage']

    newtime = outfile.variables['time']
    newstage = outfile.variables['stage']

    if last is None:
        last = len(time)

    selection = range(first, last, step)
    for i, j in enumerate(selection):
        log.critical('Copying timestep %d of %d (%f)'
                     % (j, last-first, time[j]))
        newtime[i] = time[j]
        newstage[i,:] = stage[j,:]

    # Close
    infile.close()
    outfile.close()