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data_req.py
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data_req.py
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#!/usr/bin/env python
# This file is part of ppnc.
# ppnc Copyright (C) 2015 University of Cambridge
# Ppnc is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
# Ppnc is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License along
# with ppnc. If not, see <http://www.gnu.org/licenses/>.
__version__ = "$Format:%h$"
import iris
import numpy
import config.tweakables as tweakables
from config.req_data import req_data
class req():
def __init__(self, STASH):
self.STASH = STASH
self.reqStdName = req_data[self.STASH]['req_standard_name']
self.reqLongName = req_data[self.STASH]['req_long_name']
self.cnvfact = req_data[self.STASH]['conversion_factor']
self.var_name = req_data[self.STASH]['var_name']
self.units = req_data[self.STASH]['units']
self.is3D = True
self.regridded = False
# Pull in a comment from req_data if set
if 'comment' in req_data[self.STASH]:
self.comment = req_data[self.STASH]['comment']
else:
self.comment = None
if 'valid_range' in req_data[self.STASH]:
self.valid_range = req_data[self.STASH]['valid_range']
else:
self.valid_range = None
if not self.reqStdName in iris.std_names.STD_NAMES:
iris.std_names.STD_NAMES[self.reqStdName] = {'canonical_units': str(self.units)}
def callback(self, cube, field, filename):
if cube.attributes['STASH'] == self.STASH:
cube.attributes['conversion_factor'] = self.cnvfact
try:
cube.standard_name = self.reqStdName
except ValueError:
cube.long_name = self.reqStdName
cube.units = req_data[self.STASH]['units']
def convert(self, cube, args):
if cube.attributes['STASH'] == self.STASH:
# make it 64-bit
cube.data = cube.data.astype(dtype='float64')
# If conversion_factor not 1, convert
if self.cnvfact != 1:
if cube.units.is_dimensionless() or cube.units.is_time():
cube.data = (cube.data / self.cnvfact)
elif 'm-3' in cube.units.definition:
if args.cellfile is not None:
cellvolume = iris.load(args.cellfile)
cube.data = numpy.divide(cube.data, cellvolume[0].data)
else:
raise ValueError("Need to specify Grid Cell Volume File")
try:
cube.standard_name = self.reqStdName
except ValueError:
pass
cube.long_name = self.reqLongName
cube.units = req_data[self.STASH]['units']
return cube
def create_new_cubes(self, cubes):
stashcube = cubes.extract(iris.AttributeConstraint(STASH=self.STASH))[0]
# what are the dimensions of this cube
if stashcube.ndim == 3:
self.is3D = False
elif stashcube.ndim == 4:
self.is3D = True
newcube = self.convert_pressure(stashcube, cubes)
return self.add_metadata(newcube, stashcube)
def mask_outside_valid_range(self, data):
# If we have a valid range, mask things outside it.
if self.valid_range:
return numpy.ma.masked_outside(data, *self.valid_range)
else:
return data
def convert_pressure(self, stashcube, cubes):
if self.is3D:
import pressureconv
"""Takes two cubes, vv and air_pressure, converts to pressure levels"""
# Tolerance for checking whether cubes are equal. These just happen to
# be the numpy defaults
rtol = 1e-05
atol = 1e-08
# Check if heights are the same, otherwise exit with error
if not cubes[0].coords('level_height') == []:
if not numpy.allclose(cubes[0].coords('level_height')[0].points, cubes[1].coords('level_height')[0].points, rtol=rtol, atol=atol):
raise ValueError("Coordinates level_height for %s and %s do not match!" % (cubes[0].name(), cubes[1].name()))
# check if lat/lon are different between vv and pp cubes
if not compare_lat_lon(cubes=cubes, rtol=rtol, atol=atol):
# Regrid
pressure = (cubes.extract(iris.Constraint('air_pressure'))[0])
pp = pressure.regrid(stashcube, iris.analysis.Linear()).data
self.regridded = True
else:
pp = (cubes.extract(iris.Constraint('air_pressure'))[0]).data
vv = stashcube.data
# Use f2py pressureconv to convert to plevels
newvv = numpy.ma.array(data=pressureconv.convert_height2pressure(plevels=tweakables.plevels, vv=vv, pp=pp, fillval=tweakables.fillval), fill_value=tweakables.fillval, dtype='float32')
newcube = iris.cube.Cube(self.mask_outside_valid_range(newvv), standard_name=self.reqStdName, var_name=self.var_name, units=self.units, attributes=None, cell_methods=None, dim_coords_and_dims=None, aux_coords_and_dims=None, aux_factories=None)
return newcube
else:
# no pressure to convert.
cubedata = self.mask_outside_valid_range(numpy.ma.array(data=stashcube.data, fill_value=tweakables.fillval, dtype='float32'))
return iris.cube.Cube(cubedata, standard_name=self.reqStdName, var_name=self.var_name, units=self.units, attributes=None, cell_methods=None, dim_coords_and_dims=None, aux_coords_and_dims=None, aux_factories=None)
def add_metadata(self, cube, orig_cube):
# Preserve the metadata
cube.metadata = orig_cube.metadata
cube.attributes['cell_measures'] = 'area: areacella'
cube.var_name = self.var_name
# Provide - cell_methods = "time: mean"
cube.cell_methods = [iris.coords.CellMethod('mean', 'time')]
# Make the coords
if self.is3D:
newcoords = iris.coords.DimCoord(tweakables.plevels,
standard_name='air_pressure',
var_name='plev',
attributes={'positive': 'down'},
units=iris.unit.Unit('Pa'))
latcoords = coords_to_float64(orig_cube.coords('latitude')[0])
longcorrds = coords_to_float64(orig_cube.coords('longitude')[0])
# Rename them
latcoords.var_name = 'lat'
longcorrds.var_name = 'lon'
new_time_unit = iris.unit.Unit('days since 1960-01-01', calendar='360_day')
orig_cube.coords('time')[0].convert_units(new_time_unit)
cube.add_dim_coord(orig_cube.coords('time')[0], 0)
cube.coords('time')[0].var_name = 'time'
# Stick them on the cube
if self.is3D:
cube.add_dim_coord(newcoords, 1)
cube.add_dim_coord(latcoords, 2)
cube.add_dim_coord(longcorrds, 3)
else:
cube.add_dim_coord(latcoords, 1)
cube.add_dim_coord(longcorrds, 2)
for coord in cube.coords():
if coord.bounds is None:
set_bounds(coord)
# Prevent source from being overwritten.
cube.attributes.pop('source')
cube.attributes['associated_files'] = "baseURL: http://www.met.reading.ac.uk/ccmi/ gridspecFile: gridspec_atmos_fx_UMUKCA-UCAM_refC2_r0i0p0.nc"
if self.comment is not None:
cube.attributes['comment'] = self.comment
if cube.standard_name.startswith('mole_fraction'):
cube.attributes['comment'] = "Model output is in mass_fraction, and so data is converted to mole_fraction by dividing by conversion_factor. "
elif not 'comment' in cube.attributes:
# If it isn't set, create a blank entry.
cube.attributes['comment'] = ""
if self.regridded:
cube.attributes['comment'] = cube.attributes['comment'] + "Due a mismatch in the latitude/longitude grids between the pressure field and the variable field, the pressure field was bilinearly interpolated in the horizontal prior to the interpolation from model levels onto pressure levels."
return cube
def compare_lat_lon(cubes, rtol, atol):
# Are there the same number of points in both
if len(cubes[0].coords('latitude')[0].points) != len(cubes[1].coords('latitude')[0].points):
return False
# Do the points match
elif not ((numpy.allclose(cubes[0].coords('latitude')[0].points, cubes[1].coords('latitude')[0].points, rtol=rtol, atol=atol)) and (numpy.allclose(cubes[0].coords('longitude')[0].points, cubes[1].coords('longitude')[0].points, rtol=rtol, atol=atol))):
return False
else:
return True
def set_bounds(coord):
# guess_bounds sets |bounds| too large
coord.guess_bounds()
if coord.var_name == 'lat':
# remove bounds >90.0 or <-90.0
newbounds = coord.bounds.copy()
newbounds[0][0] = -90.0
newbounds[-1][1] = 90.0
coord.bounds = newbounds
return coord
def coords_to_float64(coord):
coord.points = coord.points.astype(dtype='float64')
return coord