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()
descriptor.create(lat, lon, units='degrees')
return descriptor
def get_latlon_file_descriptor(self):
latLonGridFileName = str(self.datadir.join('SST_annual_1870-1900.nc'))
descriptor = LatLonGridDescriptor.read(latLonGridFileName,
latVarName='lat',
lonVarName='lon')
return (descriptor, latLonGridFileName)
def get_observation_descriptor(self, fileName): # {{{
'''
get a MeshDescriptor for the observation grid
Parameters
----------
fileName : str
observation file name describing the source grid
Returns
-------
obsDescriptor : ``MeshDescriptor``
The descriptor for the observation grid
'''
# Authors
# -------
# Xylar Asay-Davis, Luke Van Roekel
# Load Argo observational Data
dsObs = self.build_observational_dataset(fileName)
# create a descriptor of the observation grid using Lat/Lon
# coordinates
obsDescriptor = LatLonGridDescriptor.read(ds=dsObs,
latVarName='latCoord',
lonVarName='lonCoord')
dsObs.close()
return obsDescriptor # }}}
def get_observation_descriptor(self, fileName): # {{{
'''
get a MeshDescriptor for the observation grid
Parameters
----------
fileName : str
observation file name describing the source grid
Returns
-------
obsDescriptor : ``MeshDescriptor``
The descriptor for the observation grid
Authors
-------
Xylar Asay-Davis
'''
# create a descriptor of the observation grid using the lat/lon
# coordinates
obsDescriptor = LatLonGridDescriptor.read(fileName=fileName,
latVarName='lat',
lonVarName='lon')
return obsDescriptor # }}}
def get_observation_descriptor(self, fileName): # {{{
'''
get a MeshDescriptor for the observation grid
Parameters
----------
fileName : str
observation file name describing the source grid
Returns
-------
obsDescriptor : ``MeshDescriptor``
The descriptor for the observation grid
'''
# Authors
# -------
# Riley X. Brady, Xylar Asay-Davis
# create a descriptor of the observation grid using the lat/lon
# coordinates
dsObs = self.build_observational_dataset(fileName)
obsDescriptor = LatLonGridDescriptor.read(ds=dsObs,
latVarName='lat',
lonVarName='lon')
return obsDescriptor # }}}
def remap_v(prefix, inGridName, inGridFileName, inDir, inVPrefix):
cacheVFileName = '{}_merid_vel_{}.nc'.format(prefix, inGridName)
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
matGrid = loadmat(inGridFileName)
# lat/lon is a tensor grid so we can use 1-D arrays
lon = matGrid['XC'][:, 0]
lat = matGrid['YG'][0, :]
z = matGrid['RC'][:, 0]
cellFraction = matGrid['hFacS']
botIndices = get_bottom_indices(cellFraction)
with sose_v_to_nc('{}/{}'.format(inDir, inVPrefix),
cacheVFileName, lon, lat, z, cellFraction, botIndices) \
as dsV:
inDescriptor = LatLonGridDescriptor()
inDescriptor = LatLonGridDescriptor.read(cacheVFileName,
latVarName='lat',
lonVarName='lon')
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = outDescriptor.meshName
outVFileName = '{}_merid_vel_{}.nc'.format(prefix, outGridName)
mappingFileName = '{}/map_V_{}_to_{}.nc'.format(
inDir, inGridName, outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
if not os.path.exists(outVFileName):
print('Remapping meridional velocity...')
with remapper.remap(dsV, renormalizationThreshold=0.01) \
as remappedV:
print('Done.')
remappedV.attrs['history'] = ' '.join(sys.argv)
write_netcdf(remappedV, outVFileName)
def setup_obs_remapper(self, config, fieldName):
gridFileName = '{}/obsGrid.nc'.format(self.datadir)
comparisonDescriptor = \
get_lat_lon_comparison_descriptor(config)
obsDescriptor = LatLonGridDescriptor()
obsDescriptor.read(fileName=gridFileName, latVarName='lat',
lonVarName='lon')
remapper = \
get_remapper(
config=config, sourceDescriptor=obsDescriptor,
comparisonDescriptor=comparisonDescriptor,
mappingFileSection='oceanObservations',
mappingFileOption='sstClimatologyMappingFile',
mappingFilePrefix='map_obs_{}'.format(fieldName),
method=config.get('oceanObservations',
'interpolationMethod'))
return remapper
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)
def remap(ds, outDescriptor, mappingFileName, inDir, outFileName):
tempFileName1 = '{}/temp_transpose.nc'.format(inDir)
tempFileName2 = '{}/temp_remap.nc'.format(inDir)
if 'z' in ds:
print(' transposing and fixing periodicity...')
ds = ds.chunk({'Time': 4})
ds = ds.transpose('Time', 'z', 'lat', 'lon')
ds = add_periodic_lon(ds)
write_netcdf(ds, tempFileName1)
ds.close()
inDescriptor = LatLonGridDescriptor.read(tempFileName1,
latVarName='lat',
lonVarName='lon')
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
remapper.remap_file(inFileName=tempFileName1,
outFileName=tempFileName2,
overwrite=True,
renormalize=0.01)
ds = xarray.open_dataset(tempFileName2)
if 'z' in ds:
print(' transposing back...')
ds = ds.chunk({'Time': 4})
ds = ds.transpose('Time', 'x', 'y', 'z', 'nvertices')
ds.attrs['meshName'] = outDescriptor.meshName
for coord in ['x', 'y']:
ds.coords[coord] = xarray.DataArray.from_dict(
outDescriptor.coords[coord])
ds = ds.set_coords(names=['month', 'year'])
write_netcdf(ds, outFileName)
ds.close()
def _get_lat_lon_comparison_descriptor(config): # {{{
"""
Get a descriptor of the lat/lon comparison grid, used for remapping and
determining the grid name
Parameters
----------
config : instance of ``MpasAnalysisConfigParser``
Contains configuration options
Returns
-------
descriptor : ``LatLonGridDescriptor`` object
A descriptor of the lat/lon grid
"""
# Authors
# -------
# Xylar Asay-Davis
climSection = 'climatology'
comparisonLatRes = config.getWithDefault(climSection,
'comparisonLatResolution',
constants.dLatitude)
comparisonLonRes = config.getWithDefault(climSection,
'comparisonLatResolution',
constants.dLongitude)
nLat = int((constants.latmax - constants.latmin) / comparisonLatRes) + 1
nLon = int((constants.lonmax - constants.lonmin) / comparisonLonRes) + 1
lat = numpy.linspace(constants.latmin, constants.latmax, nLat)
lon = numpy.linspace(constants.lonmin, constants.lonmax, nLon)
descriptor = LatLonGridDescriptor.create(lat, lon, units='degrees')
return descriptor # }}}
# Copyright (c) 2018 UT-Battelle, LLC. All rights reserved.
#
# Additional copyright and license information can be found in the LICENSE file
# distributed with this code, or at
# https://raw.githubusercontent.com/MPAS-Dev/MPAS-Analysis/master/LICENSE
import numpy
from mpas_analysis.shared.interpolation import Remapper
from mpas_analysis.shared.grid import LatLonGridDescriptor
from mpas_analysis.shared.constants import constants
inputFileName = '/media/xylar/extra_data/analysis/output/GMPAS-QU240/' \
'remap_obs/clim/obs/mld_1.0x1.0degree.nc'
obsDescriptor = LatLonGridDescriptor.read(fileName=inputFileName,
latVarName='lat',
lonVarName='lon')
comparisonLatRes = 4.
comparisonLonRes = 4.
nLat = int((constants.latmax - constants.latmin) / comparisonLatRes) + 1
nLon = int((constants.lonmax - constants.lonmin) / comparisonLonRes) + 1
lat = numpy.linspace(constants.latmin, constants.latmax, nLat)
lon = numpy.linspace(constants.lonmin, constants.lonmax, nLon)
comparisonDescriptor = LatLonGridDescriptor.create(lat, lon, units='degrees')
remapper = Remapper(obsDescriptor,
comparisonDescriptor,
mappingFileName='map.nc')
def remap_pt_s(prefix, inGridName, inGridFileName, inDir, inTPrefix, inSPrefix,
inGammaNPrefix):
cacheTFileName = '{}_pot_temp_{}.nc'.format(prefix, inGridName)
cacheSFileName = '{}_salinity_{}.nc'.format(prefix, inGridName)
cacheGammaNFileName = '{}_neut_den_{}.nc'.format(prefix, inGridName)
config = MpasAnalysisConfigParser()
config.read('mpas_analysis/config.default')
matGrid = loadmat(inGridFileName)
# lat/lon is a tensor grid so we can use 1-D arrays
lon = matGrid['XC'][:, 0]
lat = matGrid['YC'][0, :]
z = matGrid['RC'][:, 0]
cellFraction = matGrid['hFacC']
botIndices = get_bottom_indices(cellFraction)
with sose_pt_to_nc('{}/{}'.format(inDir, inTPrefix),
cacheTFileName, lon, lat, z, cellFraction, botIndices) \
as dsT:
inDescriptor = LatLonGridDescriptor()
inDescriptor = LatLonGridDescriptor.read(cacheTFileName,
latVarName='lat',
lonVarName='lon')
outDescriptor = get_comparison_descriptor(config, 'antarctic')
outGridName = outDescriptor.meshName
outTFileName = '{}_pot_temp_{}.nc'.format(prefix, outGridName)
outSFileName = '{}_salinity_{}.nc'.format(prefix, outGridName)
outGammaNFileName = '{}_neut_den_{}.nc'.format(prefix, outGridName)
mappingFileName = '{}/map_C_{}_to_{}.nc'.format(
inDir, inGridName, outGridName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
if not os.path.exists(outTFileName):
dsT.reset_coords(names='zBot', inplace=True)
print('Remapping potential temperature...')
with remapper.remap(dsT, renormalizationThreshold=0.01) \
as remappedT:
print('Done.')
remappedT.attrs['history'] = ' '.join(sys.argv)
remappedT.set_coords(names='zBot', inplace=True)
write_netcdf(remappedT, outTFileName)
with sose_s_to_nc('{}/{}'.format(inDir, inSPrefix),
cacheSFileName, lon, lat, z, cellFraction, botIndices) \
as dsS:
if not os.path.exists(outSFileName):
dsS.reset_coords(names='zBot', inplace=True)
print('Remapping salinity...')
with remapper.remap(dsS, renormalizationThreshold=0.01) \
as remappedS:
print('Done.')
remappedS.attrs['history'] = ' '.join(sys.argv)
remappedS.set_coords(names='zBot', inplace=True)
write_netcdf(remappedS, outSFileName)
with sose_gammaN_to_nc('{}/{}'.format(inDir, inGammaNPrefix),
cacheGammaNFileName, lon, lat, z, cellFraction,
botIndices) \
as dsGammaN:
if not os.path.exists(outGammaNFileName):
dsGammaN.reset_coords(names='zBot', inplace=True)
print('Remapping neutral density...')
with remapper.remap(dsGammaN, renormalizationThreshold=0.01) \
as remappedGammaN:
print('Done.')
remappedGammaN.attrs['history'] = ' '.join(sys.argv)
remappedGammaN.set_coords(names='zBot', inplace=True)
write_netcdf(remappedGammaN, outGammaNFileName)
'SouthernOcean/SOSE/monthly/SALT_mnthlyBar.0000000100'
inGridFileName = '/media/xylar/extra_data/data_overflow/observations/' \
'SouthernOcean/SOSE/grid.mat'
prefix = 'SOSE_2005-2010_monthly_'
cacheTFileName = '{}_pot_temp_{}.nc'.format(prefix, inGridName)
cacheSFileName = '{}_salinity_{}.nc'.format(prefix, inGridName)
outTFileName = '{}_pot_temp_{}.nc'.format(prefix, outGridName)
outSFileName = '{}_salinity_{}.nc'.format(prefix, outGridName)
config = MpasAnalysisConfigParser()
config.read('config.default')
inDescriptor = LatLonGridDescriptor()
if not os.path.exists(cacheTFileName) or not os.path.exists(cacheSFileName):
matGrid = loadmat(inGridFileName)
# lat/lon is a tensor grid so we can use 1-D arrays
lon = matGrid['XC'][:, 0]
lat = matGrid['YC'][0, :]
z = matGrid['RC'][:, 0]
cellFraction = matGrid['hFacC']
botIndices = get_bottom_indices(cellFraction)
if os.path.exists(cacheTFileName):
dsT = xarray.open_dataset(cacheTFileName)
else:
field, botField = get_monthly_average(inTFileName)