def setup_config(self):
configPath = self.datadir.join('config.QU240')
config = MpasAnalysisConfigParser()
config.read(str(configPath))
config.set('input', 'baseDirectory', str(self.datadir))
config.set('output', 'baseDirectory', str(self.test_dir))
return config
def setup_config(self):
configPath = self.datadir.join('config.remap_obs')
config = MpasAnalysisConfigParser()
config.read(str(configPath))
config.set('input', 'baseDirectory', str(self.datadir))
config.set('diagnostics', 'baseDirectory', str(self.datadir))
config.set('oceanObservations', 'obsSubdirectory', '.')
config.set('output', 'baseDirectory', str(self.test_dir))
return config
def get_latlon_array_descriptor(self):
configPath = str(self.datadir.join('config.analysis'))
config = MpasAnalysisConfigParser()
config.read(configPath)
lat = numpy.array(
config.getExpression('interpolate', 'lat', usenumpyfunc=True))
lon = numpy.array(
config.getExpression('interpolate', 'lon', usenumpyfunc=True))
descriptor = LatLonGridDescriptor.create(lat, lon, units='degrees')
return descriptor
def remap(inDir, outDir):
inGridName = 'SouthernOcean_0.25x0.125degree'
inFileName = '{}/Schmidtko_et_al_2014_bottom_PT_S_PD_{}.nc'.format(
inDir, inGridName)
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
inDescriptor = LatLonGridDescriptor()
inDescriptor = LatLonGridDescriptor.read(inFileName,
latVarName='lat',
lonVarName='lon')
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = outDescriptor.meshName
outFileName = '{}/Schmidtko_et_al_2014_bottom_PT_S_PD_{}.nc'.format(
outDir, outGridName)
mappingFileName = '{}/map_{}_to_{}.nc'.format(inDir, inGridName,
outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
if not os.path.exists(outFileName):
print('Remapping...')
with xarray.open_dataset(inFileName) as dsIn:
with remapper.remap(dsIn, renormalizationThreshold=0.01) \
as remappedMLD:
print('Done.')
remappedMLD.attrs['history'] = ' '.join(sys.argv)
write_netcdf(remappedMLD, outFileName)
class TestMPASAnalysisConfigParser(TestCase):
def setup_config(self):
configPath = self.datadir.join('config.analysis')
self.config = MpasAnalysisConfigParser()
self.config.read(str(configPath))
def check_container(self, container, container_type, item_type):
assert isinstance(container, container_type)
for item in container:
assert isinstance(item, item_type)
def test_read_config(self):
self.setup_config()
colorMapName = self.config.get('sst_modelvsobs', 'cmapDiff')
self.assertEqual(colorMapName, 'coolwarm')
self.assertEqual(self.config.getint('Test', 'testInt'), 15)
self.assertEqual(self.config.getExpression('Test', 'testInt'), 15)
self.assertEqual(self.config.getfloat('Test', 'testFloat'), 18.0)
self.assertEqual(self.config.getExpression('Test', 'testFloat'), 18.0)
self.assertEqual(self.config.getfloat('Test', 'testFloat2'), 3.)
self.assertEqual(self.config.getExpression('Test', 'testFloat2'), 3.)
self.assertEqual(self.config.getboolean('Test', 'testBool'), True)
self.assertEqual(self.config.getExpression('Test', 'testBool'), True)
testList = self.config.getExpression('sst_modelvsobs',
'cmapIndicesModelObs')
self.check_container(testList, list, int)
self.assertEqual(testList, [0, 40, 80, 110, 140, 170, 200, 230, 255])
testList = self.config.getExpression('sst_modelvsobs',
'cmapIndicesModelObs',
elementType=float)
self.check_container(testList, list, float)
self.assertEqual(testList,
[0., 40., 80., 110., 140., 170., 200., 230., 255.])
testList = self.config.getExpression('sst_modelvsobs',
'comparisonTimes')
self.check_container(testList, list, str)
self.assertEqual(testList, ['JFM', 'JAS', 'ANN'])
testList = self.config.getExpression('Test', 'testList')
self.check_container(testList, list, float)
self.assertEqual(testList, [0.5, 0.1, 0.5])
testTuple = self.config.getExpression('Test', 'testTuple')
assert isinstance(testTuple, tuple)
self.assertEqual(testTuple, (5, 0.1, 'string'))
testDict = self.config.getExpression('Test', 'testDict')
assert isinstance(testDict, dict)
self.assertEqual(testDict, {
'key1': 'string',
'key2': -12,
'key3': False
})
with six.assertRaisesRegex(
self, configparser.NoOptionError,
"No option 'doesntexist' in section: 'Test'"):
self.config.getExpression(str('Test'), str('doesntexist'))
@requires_numpy
def test_read_config_numpy(self):
self.setup_config()
# tests numpy evaluation capability
import numpy as np
for testname in ['testNumpyarange' + str(ii) for ii in np.arange(3)]:
self.assertArrayEqual(
self.config.getExpression('TestNumpy',
testname,
usenumpyfunc=True),
np.arange(0, 1, 10))
for testname in ['testNumpylinspace' + str(ii) for ii in np.arange(3)]:
self.assertArrayEqual(
self.config.getExpression('TestNumpy',
testname,
usenumpyfunc=True),
np.linspace(0, 1, 10))
for testNumpy in ['testNumpypi' + str(ii) for ii in np.arange(3)] + \
['testNumpyPi']:
self.assertEqual(
self.config.getExpression('TestNumpy',
testNumpy,
usenumpyfunc=True), np.pi)
with six.assertRaisesRegex(
self, AssertionError,
"'__' is not allowed in .* for `usenumpyfunc=True`"):
self.config.getExpression('TestNumpy',
'testBadStr',
usenumpyfunc=True),
def test_get_with_default(self):
self.setup_config()
def check_get_with_default(name, value, dtype):
# test an options that doesn't exist using getWithDefault
var = self.config.getWithDefault('sst_modelvsobs', name, value)
assert isinstance(var, dtype)
self.assertEqual(var, value)
# test several types with getWithDefault
check_get_with_default(name='aBool', value=True, dtype=bool)
check_get_with_default(name='anInt', value=1, dtype=six.integer_types)
check_get_with_default(name='aFloat', value=1.0, dtype=float)
check_get_with_default(name='aList', value=[1, 2, 3], dtype=list)
check_get_with_default(name='aTuple', value=(1, 2, 3), dtype=tuple)
check_get_with_default(name='aDict', value={'blah': 1}, dtype=dict)
check_get_with_default(name='aStr',
value='blah',
dtype=six.string_types)
def main():
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument("-i",
"--inDir",
dest="inDir",
required=True,
help="Directory where intermediate files used in "
"processing should be downloaded")
parser.add_argument("-o",
"--outDir",
dest="outDir",
required=True,
help="Directory where final preprocessed observation "
"are stored")
args = parser.parse_args()
date = '20190603'
inGridName = 'SouthernOcean_0.167x0.167degree_{}'.format(date)
inTPrefix = 'THETA_mnthlyBar.0000000100'
inSPrefix = 'SALT_mnthlyBar.0000000100'
inMLDPrefix = 'MLD_mnthlyBar.0000000100'
inUPrefix = 'UVEL_mnthlyBar.0000000100'
inVPrefix = 'VVEL_mnthlyBar.0000000100'
inGammaNPrefix = 'GAMMA_mnthlyBar.0000000100'
# size in km of the polar stereographic grid
antarcticStereoWidth = 10000
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
config.set('climatology', 'comparisonAntarcticStereoWidth',
'{}'.format(antarcticStereoWidth))
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = '{}_{}'.format(outDescriptor.meshName, date)
inPrefixes = [
inTPrefix, inSPrefix, inMLDPrefix, inUPrefix, inVPrefix, inGammaNPrefix
]
inGridFileName = '{}/grid.mat'.format(args.inDir)
try:
os.makedirs(args.inDir)
except OSError:
pass
try:
os.makedirs(args.outDir)
except OSError:
pass
# dowload the desired file
download_files(['GRID_README.txt'],
urlBase='http://sose.ucsd.edu/DATA',
outDir=args.inDir)
urlBase = 'http://sose.ucsd.edu/DATA/SO6_V2'
fileList = ['grid.mat']
for prefix in inPrefixes:
fileList.append('{}.data.gz'.format(prefix))
fileList.append('{}.meta'.format(prefix))
download_files(fileList, urlBase, args.inDir)
unzip_sose_data(inPrefixes, args.inDir)
prefix = '{}/SOSE'.format(args.outDir)
sose_volume_to_nc(prefix, inGridName, inGridFileName, args.inDir)
prefix = '{}/SOSE_2005-2010_monthly'.format(args.outDir)
remap_pt_s(prefix, inGridName, inGridFileName, args.inDir, inTPrefix,
inSPrefix, inGammaNPrefix, outDescriptor, outGridName)
remap_mld(prefix, inGridName, inGridFileName, args.inDir, inMLDPrefix,
outDescriptor, outGridName)
remap_u(prefix, inGridName, inGridFileName, args.inDir, inUPrefix,
outDescriptor, outGridName)
remap_v(prefix, inGridName, inGridFileName, args.inDir, inVPrefix,
outDescriptor, outGridName)
compute_vel_mag(prefix, inGridName, args.inDir, outGridName)
compute_pot_density(prefix, inGridName, args.inDir, outGridName)
resolution.
'''
from mpas_analysis.shared.interpolation import Remapper
from mpas_analysis.shared.grid import MpasMeshDescriptor
from mpas_analysis.shared.climatology import get_comparison_descriptor
from mpas_analysis.configuration import MpasAnalysisConfigParser
# replace with the MPAS mesh name
inGridName = 'oQU240'
# replace with the path to the desired mesh or restart file
inGridFileName = '/media/xylar/extra_data/analysis/edison/G-QU240-master-intel/run/mpaso.rst.0001-01-06_00000.nc'
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
# replace 1.0 with the desired resolution of the output mesh
config.set('climatology', 'comparisonLatResolution', '1.0')
config.set('climatology', 'comparisonLonResolution', '1.0')
inDescriptor = MpasMeshDescriptor(inGridFileName, inGridName)
outDescriptor = get_comparison_descriptor(config, 'latlon')
outGridName = outDescriptor.meshName
mappingFileName = 'map_{}_to_{}.nc'.format(inGridName, outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')