def _extrap_model(config, modelFolder):
resExtrap = get_res(config, extrap=True)
resFinal = get_res(config, extrap=False)
hres = get_horiz_res(config)
modelName = config.get('model', 'name')
inFileName = '{}/{}_temperature_{}.nc'.format(modelFolder, modelName,
resExtrap)
bedMaskFileName = '{}/bed_mask_{}.nc'.format(modelFolder, resExtrap)
bedFileName = 'bedmap2/bedmap2_{}.nc'.format(hres)
basinNumberFileName = 'imbie/basinNumbers_{}.nc'.format(hres)
make_3D_bed_mask(inFileName, bedMaskFileName, bedFileName)
for fieldName in ['temperature', 'salinity']:
inFileName = '{}/{}_{}_{}.nc'.format(modelFolder, modelName, fieldName,
resExtrap)
outFileName = '{}/{}_{}_{}_extrap_horiz.nc'.format(
modelFolder, modelName, fieldName, resExtrap)
progressDir = '{}/progress_{}'.format(modelFolder, fieldName)
matrixDir = '{}/matrices'.format(modelName.lower())
extrap_horiz(config, inFileName, outFileName, fieldName, bedFileName,
basinNumberFileName, bedMaskFileName, progressDir,
matrixDir)
for fieldName in ['temperature', 'salinity']:
inFileName = '{}/{}_{}_{}_extrap_horiz.nc'.format(
modelFolder, modelName, fieldName, resExtrap)
outFileName = '{}/{}_{}_{}_extrap_vert.nc'.format(
modelFolder, modelName, fieldName, resExtrap)
extrap_vert(config, inFileName, outFileName, fieldName)
inFileNames = {}
outFileNames = {}
for fieldName in ['temperature', 'salinity']:
inFileNames[fieldName] = '{}/{}_{}_{}_extrap_vert.nc'.format(
modelFolder, modelName, fieldName, resExtrap)
outFileNames[fieldName] = '{}/{}_{}_{}_extrap_vert.nc'.format(
modelFolder, modelName, fieldName, resFinal)
remap_vertical(config, inFileNames, outFileNames, extrap=False)
for fieldName in ['temperature', 'salinity']:
inFileName = '{}/{}_{}_{}_extrap_vert.nc'.format(
modelFolder, modelName, fieldName, resFinal)
outFileName = '{}/{}_{}_{}.nc'.format(modelFolder, modelName,
fieldName, resFinal)
progressDir = '{}/progress_{}'.format(modelFolder, fieldName)
matrixDir = '{}/matrices'.format(modelName.lower())
extrap_grounded_above_sea_level(config, inFileName, outFileName,
fieldName, progressDir, matrixDir)
def make_imbie_masks(config):
'''
Download geojson files defining IMBIE basins and create masks that extend
these basins into the open ocean
'''
res = get_horiz_res(config)
try:
os.makedirs('imbie')
except OSError:
pass
if os.path.exists('imbie/basinNumbers_{}.nc'.format(res)):
# we're already done
return
print('Building IMBIE basin masks...')
basins = {
'A-Ap': ['A-Ap'],
'Ap-B': ['Ap-B'],
'B-C': ['B-C'],
'C-Cp': ['C-Cp'],
'Cp-D': ['Cp-D'],
'D-Dp': ['D-Dp'],
'Dp-E': ['Dp-E'],
'E-F': ['E-Ep', 'Ep-F'],
'F-G': ['F-G'],
'G-H': ['G-H'],
'H-Hp': ['H-Hp'],
'Hp-I': ['Hp-I'],
'I-Ipp': ['I-Ipp'],
'Ipp-J': ['Ipp-J'],
'J-K': ['J-Jpp', 'Jpp-K'],
'K-A': ['K-A']
}
bedFileName = 'bedmap2/bedmap2_{}.nc'.format(res)
_download_imbie()
images.write_basin_images(res, bedFileName, basins)
extend.extend_imbie_masks(res, basins, bedFileName)
print(' Done.')
def _remap(config, decades):
res = get_res(config)
hres = get_horiz_res(config)
bothExist = True
for fieldName in ['temperature', 'salinity']:
outFileName = 'woa/woa_{}_{}_{}.nc'.format(fieldName, decades, res)
if not os.path.exists(outFileName):
bothExist = False
break
if bothExist:
return
print(' Remapping to {} grid...'.format(res))
for fieldName in ['temperature', 'salinity']:
inFileName = 'woa/woa18_{}_{}_interp_z.nc'.format(decades, fieldName)
outGridFileName = 'ismip6/{}_grid.nc'.format(hres)
outFileName = 'woa/woa_{}_{}_{}.nc'.format(fieldName, decades, res)
if os.path.exists(outFileName):
continue
print(' {}'.format(outFileName))
varName = fieldName
inDescriptor = get_lat_lon_descriptor(inFileName)
outDescriptor = get_antarctic_descriptor(outGridFileName)
mappingFileName = 'woa/map_{}_to_{}.nc'.format(inDescriptor.meshName,
outDescriptor.meshName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
ds = xarray.open_dataset(inFileName)
ds = ds.rename({varName: fieldName})
dsOut = remapper.remap(ds, renormalizationThreshold=0.1)
for attrName in ['units', 'standard_name', 'long_name']:
dsOut[fieldName].attrs[attrName] = ds[fieldName].attrs[attrName]
dsOut.z.attrs = ds.z.attrs
dsOut.to_netcdf(outFileName)
def bedmap2_to_ismip6_grid(config):
try:
os.makedirs('bedmap2')
except OSError:
pass
try:
os.makedirs('ismip6')
except OSError:
pass
res = get_horiz_res(config)
inFileName = 'bedmap2/bedmap2.nc'
outGridFileName = 'ismip6/{}_grid.nc'.format(res)
outFileName = 'bedmap2/bedmap2_{}.nc'.format(res)
_bedmap2_bin_to_netcdf(inFileName)
_write_ismip6_grid(config, outGridFileName)
_remap(inFileName, outGridFileName, outFileName, res)
def extrap_obs(config, decades):
resExtrap = get_res(config, extrap=True)
resFinal = get_res(config, extrap=False)
hres = get_horiz_res(config)
inFileName = f'obs/obs_temperature_{decades}_{resExtrap}.nc'
bedMaskFileName = f'obs/bed_mask_{resExtrap}.nc'
bedFileName = f'bedmap2/bedmap2_{hres}.nc'
basinNumberFileName = f'imbie/basinNumbers_{hres}.nc'
make_3D_bed_mask(inFileName, bedMaskFileName, bedFileName)
matrixDirs = dict()
progressDirs = dict()
for fieldName in ['temperature', 'salinity']:
progressDirs[fieldName] = f'obs/progress_{fieldName}'
matrixDirs[fieldName] = f'obs/matrices_{fieldName}'
for fieldName in ['temperature', 'salinity']:
progressDir = progressDirs[fieldName]
matrixDir = matrixDirs[fieldName]
inFileName = f'{progressDir}/obs_{fieldName}_{decades}_{resExtrap}.nc'
outFileName = f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resExtrap}_extrap_horiz.nc'
extrap_horiz(config, inFileName, outFileName, fieldName, bedFileName,
basinNumberFileName, bedMaskFileName, progressDir,
matrixDir)
for fieldName in ['temperature', 'salinity']:
progressDir = progressDirs[fieldName]
inFileName = f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resExtrap}_extrap_horiz.nc'
outFileName = f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resExtrap}_extrap_vert.nc'
extrap_vert(config, inFileName, outFileName, fieldName)
tempFileName = \
f'{progressDir}/obs_temperature_{decades}_{resExtrap}_extrap_vert.nc'
salinFileName = \
f'{progressDir}/obs_salinity_{decades}_{resExtrap}_extrap_vert.nc'
outFileName = \
f'{progressDir}/' \
f'obs_thermal_forcing_{decades}_{resExtrap}_extrap_vert.nc'
compute_thermal_forcing(tempFileName, salinFileName, outFileName)
inFileNames = {}
outFileNames = {}
for fieldName in ['temperature', 'salinity']:
progressDir = progressDirs[fieldName]
inFileNames[fieldName] = \
f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resExtrap}_extrap_vert.nc'
outFileNames[fieldName] = \
f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resFinal}_extrap_vert.nc'
remap_vertical(config, inFileNames, outFileNames, extrap=False)
for fieldName in ['temperature', 'salinity']:
progressDir = progressDirs[fieldName]
matrixDir = matrixDirs[fieldName]
inFileName = f'{progressDir}/' \
f'obs_{fieldName}_{decades}_{resFinal}_extrap_vert.nc'
outFileName = f'obs/obs_{fieldName}_{decades}_{resFinal}.nc'
extrap_grounded_above_sea_level(config, inFileName, outFileName,
fieldName, progressDir, matrixDir)
def _bin_en4(config, inVarName, outVarName, startYear, endYear):
hres = get_horiz_res(config)
dz = config.getfloat('grid', 'dzExtrap')
nz = config.getint('grid', 'nzExtrap')
zOut = dz*numpy.arange(nz+1)
z = 0.5*(zOut[0:-1] + zOut[1:])
z_bnds = numpy.zeros((len(z), 2))
z_bnds[:, 0] = zOut[0:-1]
z_bnds[:, 1] = zOut[1:]
ds = xarray.open_dataset('ismip6/{}_grid.nc'.format(hres))
ds['z'] = (('z',), z)
ds.z.attrs['units'] = 'meters'
ds.z.attrs['bounds'] = 'z_bnds'
ds.z.attrs['standard_name'] = 'depth'
ds.z.attrs['positive'] = 'up'
ds.z.attrs['axis'] = 'Z'
ds['z_bnds'] = (('z', 'nbounds'), z_bnds)
ds.z_bnds.attrs['comment'] = 'depth bounds'
xMin = ds.x[0].values
yMin = ds.y[0].values
zMin = z[0]
dx = ds.x[1].values - ds.x[0].values
nx = ds.sizes['x']
ny = ds.sizes['y']
nz = ds.sizes['z']
outField = numpy.zeros((nz, ny, nx))
entryCount = numpy.zeros((nz, ny, nx), dtype=int)
attrs = None
proj = get_antarctic_stereographic_projection()
X, Y = numpy.meshgrid(ds.x.values, ds.y.values)
Lon, Lat = proj(X, Y, inverse=True)
ds['lon'] = (('y', 'x'), Lon)
ds.lon.attrs['units'] = 'degrees'
ds['lat'] = (('y', 'x'), Lat)
ds.lat.attrs['units'] = 'degrees'
fileList = sorted(glob.glob('en4/profiles/*.nc'))
print(' Binning EN4 {} profiles...'.format(outVarName))
widgets = [' ', progressbar.Percentage(), ' ',
progressbar.Bar(), ' ', progressbar.ETA()]
bar = progressbar.ProgressBar(widgets=widgets,
maxval=len(fileList)).start()
for index, fileName in enumerate(fileList):
dsProfile = xarray.open_dataset(fileName)
lat = dsProfile.LATITUDE.values
lon = dsProfile.LONGITUDE.values
inField = dsProfile['{}_CORRECTED'.format(inVarName)].values
quality = dsProfile['{}_CORRECTED_QC'.format(inVarName)].values
if attrs is None:
attrs = dsProfile['{}_CORRECTED'.format(inVarName)].attrs
x, y = proj(lon, lat)
depths = dsProfile.DEPH_CORRECTED.values
lat = numpy.maximum(lat, -75.)
for profile in range(depths.shape[0]):
xBin = int((x[profile]-xMin)/dx)
yBin = int((y[profile]-yMin)/dx)
if xBin < 0 or xBin >= nx:
continue
if yBin < 0 or yBin >= ny:
continue
for level in range(depths.shape[1]):
if quality[profile, level] != b'1':
continue
depth = depths[profile, level]
if numpy.isnan(depth):
continue
zBin = int((depth-zMin)/dz)
if zBin < 0 or zBin >= nz:
continue
outField[zBin, yBin, xBin] += inField[profile, level]
entryCount[zBin, yBin, xBin] += 1
bar.update(index+1)
bar.finish()
mask = entryCount > 0
outField[mask] /= entryCount[mask]
outField[numpy.logical_not(mask)] = numpy.nan
ds[outVarName] = (('z', 'y', 'x'), outField)
for attr in ['units', 'long_name', 'comment']:
ds[outVarName].attrs[attr] = attrs[attr]
return ds
def _remap(config, modelFolder):
res = get_res(config)
hres = get_horiz_res(config)
modelName = config.get('model', 'name')
inFileNames = {}
outFileNames = {}
bothExist = True
for fieldName in ['temperature', 'salinity']:
inFileNames[fieldName] = \
'{}/{}_{}_interp_z.nc'.format(modelFolder, modelName, fieldName)
outFileNames[fieldName] = \
'{}/{}_{}_{}.nc'.format(modelFolder, modelName, fieldName, res)
if not os.path.exists(outFileNames[fieldName]):
bothExist = False
if bothExist:
return
print(' Remapping to {} grid...'.format(res))
for fieldName in inFileNames:
inFileName = inFileNames[fieldName]
outFileName = outFileNames[fieldName]
if os.path.exists(outFileName):
continue
outGridFileName = 'ismip6/{}_grid.nc'.format(hres)
print(' {}'.format(outFileName))
progressDir = '{}/progress_remap_{}'.format(modelFolder, fieldName)
try:
os.makedirs(progressDir)
except OSError:
pass
ds = xarray.open_dataset(inFileName)
if len(ds.lon.dims) == 1:
inDescriptor = LatLonGridDescriptor.read(
inFileName, latVarName='lat', lonVarName='lon')
else:
assert(len(ds.lon.dims) == 2)
inDescriptor = LatLon2DGridDescriptor.read(
inFileName, latVarName='lat', lonVarName='lon')
inDescriptor.regional = True
outDescriptor = get_antarctic_descriptor(outGridFileName)
mappingFileName = '{}/map_{}_to_{}.nc'.format(
modelName.lower(), inDescriptor.meshName,
outDescriptor.meshName)
remapper = Remapper(inDescriptor, outDescriptor, mappingFileName)
remapper.build_mapping_file(method='bilinear')
ds = ds.drop(['lat', 'lon'])
nt = ds.sizes['time']
widgets = [' ', progressbar.Percentage(), ' ',
progressbar.Bar(), ' ', progressbar.ETA()]
bar = progressbar.ProgressBar(widgets=widgets,
maxval=nt).start()
for tIndex in range(nt):
progressFileName = '{}/{}_t_{}.nc'.format(
progressDir, modelName, tIndex)
if os.path.exists(progressFileName):
bar.update(tIndex+1)
continue
dsIn = ds.isel(time=tIndex)
dsOut = remapper.remap(dsIn, renormalizationThreshold=0.1)
dsOut = dsOut.transpose('z', 'y', 'x')
for attrName in ['units', 'standard_name', 'long_name']:
if attrName in ds[fieldName].attrs:
dsOut[fieldName].attrs[attrName] = \
ds[fieldName].attrs[attrName]
dsOut.z.attrs = ds.z.attrs
dsOut.to_netcdf(progressFileName)
bar.update(tIndex+1)
bar.finish()
dsOut = xarray.open_mfdataset(
'{}/{}_t_*.nc'.format(progressDir, modelName), concat_dim='time')
dsOut['z_bnds'] = ds.z_bnds
dsOut.to_netcdf(outFileName)
def _extrap_model(config, modelFolder):
resExtrap = get_res(config, extrap=True)
resFinal = get_res(config, extrap=False)
hres = get_horiz_res(config)
modelName = config.get('model', 'name')
fields = config.get('model', 'fields')
fields = fields.replace(',', ' ').split()
basin = config.get('model', 'basin')
combineBasins = config.getboolean('model', 'combineBasins')
inFileName = f'{modelFolder}/remap/{modelName}_temperature_{resExtrap}.nc'
bedMaskFileName = f'{modelFolder}/bed_mask_{resExtrap}.nc'
bedFileName = f'bedmap2/bedmap2_{hres}.nc'
basinNumberFileName = f'imbie/basinNumbers_{hres}.nc'
make_3D_bed_mask(inFileName, bedMaskFileName, bedFileName)
matrixDir = os.path.join(modelName.lower(), 'matrices')
progressDirs = dict()
for fieldName in fields:
progressDirs[fieldName] = f'{modelFolder}/progress_{fieldName}'
for fieldName in fields:
progressDir = progressDirs[fieldName]
inFileName = f'{modelFolder}/remap/' \
f'{modelName}_{fieldName}_{resExtrap}.nc'
outFileName = f'{progressDir}/' \
f'{modelName}_{fieldName}_{resExtrap}_extrap_horiz.nc'
extrap_horiz(config,
inFileName,
outFileName,
fieldName,
bedFileName,
basinNumberFileName,
bedMaskFileName,
progressDir,
matrixDir,
basin=basin,
combine=combineBasins)
if not combineBasins:
return
for fieldName in fields:
progressDir = progressDirs[fieldName]
inFileName = f'{progressDir}/' \
f'{modelName}_{fieldName}_{resExtrap}_extrap_horiz.nc'
outFileName = f'{progressDir}/' \
f'{modelName}_{fieldName}_{resExtrap}_extrap_vert.nc'
extrap_vert(config, inFileName, outFileName, fieldName)
inFileNames = {}
outFileNames = {}
for fieldName in fields:
progressDir = progressDirs[fieldName]
inFileNames[fieldName] = \
f'{progressDir}/' \
f'{modelName}_{fieldName}_{resExtrap}_extrap_vert.nc'
outFileNames[fieldName] = \
f'{progressDir}/' \
f'{modelName}_{fieldName}_{resFinal}_extrap_vert.nc'
remap_vertical(config, inFileNames, outFileNames, extrap=False)
for fieldName in fields:
progressDir = progressDirs[fieldName]
inFileName = f'{progressDir}/' \
f'{modelName}_{fieldName}_{resFinal}_extrap_vert.nc'
outFileName = f'{modelFolder}/{modelName}_{fieldName}_{resFinal}.nc'
extrap_grounded_above_sea_level(config, inFileName, outFileName,
fieldName, progressDir, matrixDir)
def extrap_obs(config, decades):
resExtrap = get_res(config, extrap=True)
resFinal = get_res(config, extrap=False)
hres = get_horiz_res(config)
inFileName = 'obs/obs_temperature_{}_{}.nc'.format(decades, resExtrap)
bedMaskFileName = 'obs/bed_mask_{}.nc'.format(resExtrap)
bedFileName = 'bedmap2/bedmap2_{}.nc'.format(hres)
basinNumberFileName = 'imbie/basinNumbers_{}.nc'.format(hres)
make_3D_bed_mask(inFileName, bedMaskFileName, bedFileName)
for fieldName in ['temperature', 'salinity']:
inFileName = 'obs/obs_{}_{}_{}.nc'.format(fieldName, decades,
resExtrap)
outFileName = 'obs/obs_{}_{}_{}_extrap_horiz.nc'.format(
fieldName, decades, resExtrap)
progressDir = 'obs/progress_{}'.format(fieldName)
matrixDir = 'obs/matrices_{}'.format(fieldName)
extrap_horiz(config, inFileName, outFileName, fieldName, bedFileName,
basinNumberFileName, bedMaskFileName, progressDir,
matrixDir)
for fieldName in ['temperature', 'salinity']:
inFileName = 'obs/obs_{}_{}_{}_extrap_horiz.nc'.format(
fieldName, decades, resExtrap)
outFileName = 'obs/obs_{}_{}_{}_extrap_vert.nc'.format(
fieldName, decades, resExtrap)
extrap_vert(config, inFileName, outFileName, fieldName)
tempFileName = \
'obs/obs_temperature_{}_{}_extrap_vert.nc'.format(decades, resExtrap)
salinFileName = \
'obs/obs_salinity_{}_{}_extrap_vert.nc'.format(decades, resExtrap)
outFileName = \
'obs/obs_thermal_forcing_{}_{}_extrap_vert.nc'.format(decades,
resExtrap)
compute_thermal_forcing(tempFileName, salinFileName, outFileName)
inFileNames = {}
outFileNames = {}
for fieldName in ['temperature', 'salinity']:
inFileNames[fieldName] = \
'obs/obs_{}_{}_{}_extrap_vert.nc'.format(
fieldName, decades, resExtrap)
outFileNames[fieldName] = \
'obs/obs_{}_{}_{}_extrap_vert.nc'.format(
fieldName, decades, resFinal)
remap_vertical(config, inFileNames, outFileNames, extrap=False)
for fieldName in ['temperature', 'salinity']:
inFileName = 'obs/obs_{}_{}_{}_extrap_vert.nc'.format(
fieldName, decades, resFinal)
outFileName = 'obs/obs_{}_{}_{}.nc'.format(fieldName, decades,
resFinal)
progressDir = 'obs/progress_{}'.format(fieldName)
matrixDir = 'obs/matrices_{}'.format(fieldName)
extrap_grounded_above_sea_level(config, inFileName, outFileName,
fieldName, progressDir, matrixDir)
def _bin_meop(config, inVarName, outVarName):
res = get_res(config)
outFileName = 'meop/meop_{}_{}.nc'.format(outVarName, res)
if os.path.exists(outFileName):
return
hres = get_horiz_res(config)
dz = config.getfloat('grid', 'dzExtrap')
nz = config.getint('grid', 'nzExtrap')
zOut = dz*numpy.arange(nz+1)
z = 0.5*(zOut[0:-1] + zOut[1:])
z_bnds = numpy.zeros((len(z), 2))
z_bnds[:, 0] = zOut[0:-1]
z_bnds[:, 1] = zOut[1:]
ds = xarray.open_dataset('ismip6/{}_grid.nc'.format(hres))
ds['z'] = (('z',), z)
ds.z.attrs['units'] = 'meters'
ds.z.attrs['bounds'] = 'z_bnds'
ds.z.attrs['standard_name'] = 'depth'
ds.z.attrs['positive'] = 'up'
ds.z.attrs['axis'] = 'Z'
ds['z_bnds'] = (('z', 'nbounds'), z_bnds)
ds.z_bnds.attrs['comment'] = 'depth bounds'
xMin = ds.x[0].values
yMin = ds.y[0].values
zMin = z[0]
dx = ds.x[1].values - ds.x[0].values
nx = ds.sizes['x']
ny = ds.sizes['y']
nz = ds.sizes['z']
outField = numpy.zeros((nz, ny, nx))
entryCount = numpy.zeros((nz, ny, nx), dtype=int)
attrs = None
proj = get_antarctic_stereographic_projection()
fileList = sorted(glob.glob('meop/MEOP-CTD_2018-04-10/*/DATA_ncARGO/*.nc'))
print(' Binning MEOP {} profiles...'.format(outVarName))
widgets = [' ', progressbar.Percentage(), ' ',
progressbar.Bar(), ' ', progressbar.ETA()]
bar = progressbar.ProgressBar(widgets=widgets,
maxval=len(fileList)).start()
for index, fileName in enumerate(fileList):
dsProfile = xarray.open_dataset(fileName)
lat = dsProfile.LATITUDE.values
lon = dsProfile.LONGITUDE.values
inField = dsProfile['{}_ADJUSTED'.format(inVarName)].values
quality = dsProfile['{}_ADJUSTED_QC'.format(inVarName)].values
if attrs is None:
attrs = dsProfile[inVarName].attrs
x, y = proj(lon, lat)
pressure = dsProfile.PRES.values
lat = numpy.maximum(lat, -75.)
for profile in range(pressure.shape[0]):
xBin = int((x[profile]-xMin)/dx)
yBin = int((y[profile]-yMin)/dx)
if xBin < 0 or xBin >= nx:
continue
if yBin < 0 or yBin >= ny:
continue
for level in range(pressure.shape[1]):
if quality[profile, level] != b'1':
continue
press = pressure[profile, level]
if numpy.isnan(press):
continue
depth = gsw.z_from_p(pressure[profile, level], lat[profile])
zBin = int((depth-zMin)/dz)
if zBin < 0 or zBin >= nz:
continue
outField[zBin, yBin, xBin] += inField[profile, level]
entryCount[zBin, yBin, xBin] += 1
bar.update(index+1)
bar.finish()
mask = entryCount > 0
outField[mask] /= entryCount[mask]
outField[numpy.logical_not(mask)] = numpy.nan
ds[outVarName] = (('z', 'y', 'x'), outField)
for attr in ['units', 'long_name', 'comment']:
ds[outVarName].attrs[attr] = attrs[attr]
ds.to_netcdf(outFileName)
