def _cmorize_dataset(in_file, var, cfg, out_dir):
logger.info("CMORizing variable '%s' from input file '%s'",
var['short_name'], in_file)
attributes = deepcopy(cfg['attributes'])
attributes['mip'] = var['mip']
cmor_table = cfg['cmor_table']
definition = cmor_table.get_variable(var['mip'], var['short_name'])
cube = iris.load_cube(str(in_file),
constraint=utils.var_name_constraint(var['raw']))
# Set correct names
cube.var_name = definition.short_name
if definition.standard_name:
cube.standard_name = definition.standard_name
cube.long_name = definition.long_name
# Convert units if required
cube.convert_units(definition.units)
# Set global attributes
utils.set_global_atts(cube, attributes)
logger.info("Saving CMORized cube for variable %s", cube.var_name)
utils.save_variable(cube, cube.var_name, out_dir, attributes)
return in_file
def _cmorize_dataset(in_file, var, cfg, out_dir):
logger.info("CMORizing variable '%s' from input file '%s'",
var['short_name'], in_file)
attributes = deepcopy(cfg['attributes'])
attributes['mip'] = var['mip']
cmor_table = cfg['cmor_table']
definition = cmor_table.get_variable(var['mip'], var['short_name'])
cube = iris.load_cube(str(in_file),
constraint=utils.var_name_constraint(var['raw']))
# Time has strange values, so use forecast_reference_time instead
cube.remove_coord('time')
cube.coord('forecast_reference_time').rename('time')
# The following lines are essential before applying
# the common function fix_coords
# Convert time calendar from proleptic_gregorian to gregorian
cube.coord('time').units = cf_units.Unit(
cube.coord('time').units.origin, 'gregorian')
# Set standard_names for lat and lon
cube.coord('lat').standard_name = 'latitude'
cube.coord('lon').standard_name = 'longitude'
cube = utils.fix_coords(cube)
# The above command does not return bounds for longitude
# so explicitly get them here.
cube.coord('longitude').guess_bounds()
# Set correct names
cube.var_name = definition.short_name
cube.long_name = definition.long_name
# Convert units if required
cube.units = '1'
cube.convert_units(definition.units)
# Set global attributes
utils.set_global_atts(cube, attributes)
logger.info("Saving CMORized cube for variable %s", cube.var_name)
utils.save_variable(cube, cube.var_name, out_dir, attributes)
return in_file
def test_set_global_atts_incorrect():
"""Test set global attributes."""
cube = _create_sample_cube()
global_attrs = {
'version': '2',
'tier': '3',
'source': '4',
'reference': 'acknow_author',
'comment': '6',
'project_id': '7',
}
msg = \
"".join(["All CMORized datasets need the ",
"global attributes 'dataset_id', ",
"'version', 'tier', 'source', 'reference', 'comment' and ",
"'project_id' specified in the configuration file"])
with pytest.raises(KeyError) as key_err:
utils.set_global_atts(cube, global_attrs)
assert msg in key_err
def test_set_global_atts_correct():
"""Test set global attributes."""
cube = _create_sample_cube()
global_attrs = {
'dataset_id': '1',
'version': '2',
'tier': '3',
'source': '4',
'reference': 'acknow_author',
'comment': '6',
'project_id': '7',
}
utils.set_global_atts(cube, global_attrs)
attrs = cube.attributes
assert '1 ' in attrs['title']
assert attrs['version'] == '2'
assert attrs['tier'] == '3'
assert attrs['source'] == '4'
assert attrs['reference'] == 'doi not found'
assert attrs['comment'] == '6'
assert attrs['project_id'] == '7'
def _cmorize_dataset(in_file, var, cfg, out_dir):
logger.info("CMORizing variable '%s' from input file '%s'",
var['short_name'], in_file)
attributes = deepcopy(cfg['attributes'])
attributes['mip'] = var['mip']
cmor_table = cfg['cmor_table']
definition = cmor_table.get_variable(var['mip'], var['short_name'])
cube = iris.load_cube(str(in_file),
constraint=utils.var_name_constraint(var['raw']))
# Set correct names
cube.var_name = definition.short_name
if definition.standard_name:
cube.standard_name = definition.standard_name
cube.long_name = definition.long_name
# Convert units if required
cube.convert_units(definition.units)
# Set global attributes
utils.set_global_atts(cube, attributes)
# Setting time right
cube = regrid_time(cube, 'mon')
# Set calendar to gregorian instead of proleptic gregorian
# matplotlib does not correctly format years in proleptic gregorian
old_unit = cube.coord('time').units
new_unit = Unit(old_unit.origin, calendar='gregorian')
cube.coord('time').units = new_unit
logger.info("Saving CMORized cube for variable %s", cube.var_name)
utils.save_variable(cube, cube.var_name, out_dir, attributes)
return in_file
