def __init__(self, ncfile, readertype='generic', **kwargs):
self.ncfile = ncfile
if not isinstance(readertype, basestring):
self.f = readertype(ncfile, **kwargs)
self.type = 'callable'
elif readertype=='cdms2':
self.f = cdms2.open(ncfile, **kwargs)
self.type = readertype
elif readertype=='netcdf4':
import netcdf4
self.f = netcdf4.Dataset(ncfile, **kwargs)
self.type = readertype
else:
self.f = DS(ncfile, readertype, **kwargs)
self.type = 'dataset'
def test_obs_obsmanager_project_model():
# Load manager
manager = test_obs_obsmanager_init_surf()
# Load model
f = DS(NCFILE_MANGA0, 'mars', level='surf', logger_level='error')
temp = f('temp')
f.close()
temp.id += '_surf'
# Interpolate model
otemp = manager.project_model(temp)
assert_allclose(otemp[1][0], [12.91558515, 10.58179214])
return manager
def test_obs_ncobsplatform_surf():
# Load and stack obs
obs = NcObsPlatform(NCFILE_OBS_SURF,
logger=LOGGER,
lat=(45, 47.8),
norms=[0.2, 0.1])
stacked = obs.stacked_data.copy()
assert obs.lons.shape == (3, )
assert obs.ns == 6
assert obs.ndim == 1
assert_allclose(obs.means, [0, 0], atol=1e-7)
assert obs.depths == 'surf'
assert_allclose(stacked, [2.5, 1.5, 4., 1., 1.5, 4.])
# Named norms
notnormed = obs.set_named_norms(temp=0.1)
assert obs.norms == [0.1, 0.1]
assert_allclose(obs.stacked_data[:3], 2 * stacked[:3])
assert_allclose(obs.stacked_data[3:], stacked[3:])
obs.set_named_norms(temp=0.2)
# Interpolate model
f = DS(NCFILE_MANGA0, 'mars', level=obs.depths, logger_level='error')
temp = f('temp')
sal = f('sal')
f.close()
temp.id += '_surf'
sal.id += '_surf'
otemp = obs.project_model(temp)
osal = obs.project_model(sal)
otem_true = [12.97311556, 12.91558515, 10.58179214]
assert_allclose(otemp[0], otem_true)
# Stack model
otemp[:] -= 11.5
osal[:] -= 35.5
stacked_data = obs.restack([otemp, osal])
assert stacked_data.shape == (6, 15)
assert_allclose(stacked_data[:3, 0] * obs.norms[0] + 11.5, otem_true)
return obs
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_dens` in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
dens = ds.get_dens(squeeze=True)
# Plot surface density
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(dens[-1], savefig=figfile, close=True, vmin=1025., show=False)
# For unittest
result = {'files': figfile}
"""Test :meth:`~vacumm.data.misc.dataset.Dataset.get_var` on multiple files and time selections"""
# Inits
ncfiles = "mars2d.xyt.*.nc"
# Imports
from vcmq import DS, os, map2, data_sample
# Glob pattern
result = []
ds = DS(data_sample("mars2d.xyt.*.nc"),
'mars',
logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
assert ds.get_ssh().shape == (4, 50, 50)
assert ds.get_ssh(time=("2008-08-15 06", "2008-08-15 07", 'co'),
squeeze=True).shape == (50, 50)
# With dates
ds = DS(data_sample("mars2d.xyt.%Y%m%d%H.nc"),
'mars',
logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
assert ds.get_ssh(time=("2008-08-15 06", "2008-08-15 07",
'cc')).shape == (2, 50, 50)
"""Test method :meth:`~vacumm.data.misc.dataset.Dataset.get_grid` on MENOR""" # Inits ncfile = "menor.nc" # Imports from vcmq import DS, data_sample # Open ds = DS(data_sample(ncfile), 'mars', logger_level='critical') # Read grids grid = ds.get_grid() grid_t = ds.get_grid_t() grid_u = ds.get_grid_u() grid_v = ds.get_grid_v() # Read with selection subgrid = ds.get_grid(lon=(4, 5))
"""Test :meth:`~vacumm.data.misc.dataset.Dataset.get_var` on multiple files and time selections"""
# Inits
ncfiles = "mars2d.xyt.*.nc"
# Imports
from vcmq import DS, os, map2, data_sample
# Glob pattern
result = []
ds = DS(data_sample("mars2d.xyt.*.nc"), 'mars', logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
result.append(('assertTrue', ds.get_ssh().shape==(4, 50, 50)))
result.append(('assertTrue', ds.get_ssh(time=("2008-08-15 06", "2008-08-15 07", 'co'),
squeeze=True).shape==(50, 50)))
# With dates
ds = DS(data_sample("mars2d.xyt.%Y%m%d%H.nc"), 'mars', logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
result.append(('assertTrue', ds.get_ssh(
time=("2008-08-15 06", "2008-08-15 07", 'cc')).shape==(2, 50, 50)))
# Parameters ncfile = "menor.nc" lon = (3.0, 4.5) lat = (42, 42.8) # Imports from vcmq import DS, map2, data_sample from vacumm.diag.thermdyn import mixed_layer_depth # Read temperature and depth ncfile = data_sample(ncfile) ds = DS(ncfile, "mars", lon=lon, lat=lat) temp = ds.get_temp(squeeze=1) depth = ds.get_depth(squeeze=1) # Compute MLD mld = mixed_layer_depth(temp, depth, mode="deltatemp") # Plot map2(mld, proj="merc", figsize=(6, 6), autoresize=0, colorbar_shrink=0.7, right=1, savefigs=__file__, show=False) print "Done"
"""Test :func:`~vacumm.diag.thermdyn.mixed_layer_depth` on MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, data_sample, mixed_layer_depth, rc, map2, os, code_file_name
# Read data
ds = DS(data_sample(ncfile),'mars', logger_level='critical')
temp = ds.get_temp(squeeze=True)
sal = ds.get_sal(squeeze=True)
depth = ds.get_depth(squeeze=True)
kz = ds.get_kz(squeeze=True)
# Compute MLD
kw = dict(depth=depth, format_axes=True)
mld = {}
mld['deltatemp'] = mixed_layer_depth(temp, mode='deltatemp',**kw)
mld['deltadens'] = mixed_layer_depth((temp,sal), mode='deltadens', **kw)
mld['kz'] = mixed_layer_depth(kz, mode='kz', **kw)
vmin = min([v.min() for v in mld.values()])
vmax = max([v.max() for v in mld.values()])
# Plot it
rc('font', size=8)
for i,(mode, var) in enumerate(mld.items()):
m = map2(var, fill='pcolormesh', nmax=20, vmin=vmin, vmax=vmax,
subplot=(len(mld),1,i+1), figsize=(4.1,8),
contour_linewidths=0.7, cmap='vacumm_rnb2_hymex', hspace=0.25, bottom=0.08,
title='%%(long_name)s: mode = "%s"'%mode, show=False)
if RE_MATCH_TIME(arg) and not arg.isdigit(): # date
return arg
if re.match('[\w\s]*:[\w\s]*(:[\w\s]*)?$', arg): # args to slice
return slice(*[(None if a == '' else eval(a)) for a in arg.split(':')])
arg = eval(arg)
if isinstance(arg, int): # slice at a single index
return slice(arg, (arg + 1) if arg != -1 else None)
if isinstance(arg, float): # selection of a single position
return (arg, arg, 'cob')
return arg
# Open reader or file
if args.generic:
f = DS(args.ncfile,
args.generic,
logger_level='info' if args.verbose else 'error')
else:
f = cdms2.open(args.ncfile)
# Find a variable name if not provided
if not args.var:
if args.generic:
allvars = f.dataset[0].listvariables()
else:
allvars = f.listvariables()
for var in allvars:
if 'bounds' not in var:
if args.generic:
var = '+' + var
args.var = [var]
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_variable` with level as a string"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', logger_level='critical')
tbot = ds.get_temp(level='bottom', squeeze=True)
tsurf = ds.get_temp(level='surf', squeeze=True)
# Plot bottom
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
kw = dict(contour=True,
fill='contourf',
colorbar_shrink=0.8,
cmap='cmocean_thermal',
linewidth=.3)
m = map2(tsurf,
subplot=211,
close=False,
show=False,
figsize=(5, 7),
title='Testing Dataset.get_temp(level="surf")',
**kw)
map2(tbot,
subplot=212,
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_uvgbt` on MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import data_sample, DS, N, MV2, shapiro2d, map2, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
u, v = ds.get_uvgbt()
# Mask huge values
mask = (N.ma.sqrt(u**2 + v**2) > 2.).filled(True)
for var in u, v:
var[:] = MV2.masked_where(mask, var, copy=False)
# Shapiro filter
for var in u, v:
var[:] = shapiro2d(var)
# Plot
map2((u[0], v[0]),
title='Geostrophic velocity',
quiver_samp=3,
xymasked=False,
quiver_norm=3,
contour=False,
fill=False,
figsize=(7, 7),
quiver_linewidth=.3,
class NcReader(object):
"""A generic interface to open and read a netcdf file
Examples
--------
>>> f = NcReader(ncfile, 'mars3d') # VACUMM Mars3D reader
>>> u = f('u', lon=(10, 12)) # generic var name
>>> u = f('+sst', lon=(10, 12)) # netcdf var name
>>> f.close()
>>> f = NcReader(ncfile, 'cdms2') # direct cdms2 reader
>>> u = f('u', lon=(10, 12)) # netcdf var name
>>> f.close()
>>> f = NcReader(ncfile, 'netcdf') # python netcdf4 reader
>>> u = f('u', slice(0, 10)) # <=> f['u'][:10]
>>> f.close()
"""
def __init__(self, ncfile, readertype='generic', **kwargs):
self.ncfile = ncfile
if not isinstance(readertype, basestring):
self.f = readertype(ncfile, **kwargs)
self.type = 'callable'
elif readertype=='cdms2':
self.f = cdms2.open(ncfile, **kwargs)
self.type = readertype
elif readertype=='netcdf4':
import netcdf4
self.f = netcdf4.Dataset(ncfile, **kwargs)
self.type = readertype
else:
self.f = DS(ncfile, readertype, **kwargs)
self.type = 'dataset'
def __call__(self, vname, *args, **kwargs):
if self.type=='netcdf4':
args = tuple(filter(lambda x: isinstance(x, slice), args))
return self.f[vname][args]
else:
return self.f(vname, *args, **kwargs)
def __getitem__(self, vname):
return self.f[vname]
def get_variables(self):
if self.type=='netcdf4' or self.type=='cdms2':
return self.variables.keys()
if self.type=='dataset':
return self.f.dataset[0].variables.keys()
raise SONATError('Method yet not implemented for read type "{}"'.format(self.type))
def close(self):
self.f.close()
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""Diagnostics thermodynamiques et dynamiques (:mod:`vacumm.diag.thermdyn` et :mod:`vacumm.diag.dynamics`)"""
from vcmq import DS, data_sample, map2, density, mixed_layer_depth, barotropic_geostrophic_velocity, kinetic_energy, shapiro2d
# Lecture des données de base
ds = DS(data_sample('menor.nc'))
temp = ds.get_temp(squeeze=1)
sal = ds.get_sal(squeeze=1)
depth = ds.get_depth(squeeze=1)
ssh = ds.get_ssh(squeeze=1)
# Densité
dens_surf = density(temp[-1], sal[-1]) # -> CALCULER DENSITE 3D
map2(dens_surf)
# Couche mélangée
mld = mixed_layer_depth((temp, sal), depth, mode='deltadens') # -> ESSAYER AUTRES MODES
map2(mld, vmax=600.)
# Vitesse geostrophique
# - vitesses
ug, vg = barotropic_geostrophic_velocity(ssh)
# - energie cinetique
ke = kinetic_energy((ug, vg)) # -> TESTER AVEC SSH
ke.long_name = 'Surface geostrophique kinetic energy'
ke = shapiro2d(ke)
# Parameters
ncfile = "menor.nc"
lon = (3., 4.5)
lat = (42, 42.8)
# Imports
from vcmq import DS, map2, data_sample
from vacumm.diag.thermdyn import mixed_layer_depth
# Read temperature and depth
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', lon=lon, lat=lat)
temp = ds.get_temp(squeeze=1)
depth = ds.get_depth(squeeze=1)
# Compute MLD
mld = mixed_layer_depth(temp, depth, mode='deltatemp')
# Plot
map2(mld,
proj='merc',
figsize=(6, 6),
autoresize=0,
colorbar_shrink=0.7,
right=1,
savefigs=__file__,
show=False,
close=True)
print 'Done'
"""Test :meth:`~vacumm.data.misc.dataset.Dataset.plot_transect` on MFS"""
# Inits
ncfile = "mfs.nc"
lons = (3.125,5.5)
lats = (43.4375,42.125)
# Imports
from vcmq import DS, data_sample, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), 'nemo', logger_level='critical')
# Plot transect
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
ds.plot_transect('temp', lons, lats, outaxis='dist', show=False, fill='contourf',
figsize=(6,4), savefig=figfile, top=0.9, right=0.89, close=True)
# Parameters
ncfile = "menor.nc"
lon = (3., 4.5)
lat = (42, 42.8)
# Imports
from vcmq import DS, map2, data_sample
# Read temperature and depth
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', lon=lon, lat=lat)
mld = ds.get_mld(mode='deltatemp', squeeze=1)
# Plot
map2(mld,
proj='merc',
figsize=(6, 6),
autoresize=0,
colorbar_shrink=0.7,
right=1,
savefigs=__file__,
show=False,
close=True)
print 'Done'
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_mld` with deltadens in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
mld = ds.get_mld(mode='deltadens', deltadens=0.06, squeeze=True)
# Plot surface density
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(mld,
savefig=figfile,
close=True,
show=False,
fill='pcolormesh',
cmap='vacumm_previmer',
contour=False)
# For unittest
result = {'files': figfile}
try:
lon = eval(options.lon)
except:
parser.error('--%s: wrong argument'%selname)
select[selname] = val
# Imports
from vcmq import DS, map2, MV2, data_sample
# The file
ncfile = options.ncfile
if not os.path.exists(ncfile):
ncfile = data_sample(ncfile)
if not os.path.exists(ncfile):
parser.error('File not found: '+ncfile)
# Read temperature and depth
ds = DS(ncfile, options.model, **select)
mld = ds.get_mld(mode='deltatemp', squeeze=1)
# Time average (if needed)
if mld.ndim==3:
mld = MV2.average(mld, axis=0)
# Plot
map2(mld, proj='merc', figsize=(6, 6), autoresize=0,
title=options.title, colorbar_shrink=0.7, right=1,
show=options.disp, savefig=options.outputfig, savefig_verbose=True)
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_uvgbt` on MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import data_sample, DS, N, MV2, shapiro2d, map2, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
u, v = ds.get_uvgbt()
# Mask huge values
mask = (N.ma.sqrt(u**2+v**2)>2.).filled(True)
for var in u, v:
var[:] = MV2.masked_where(mask, var, copy=False)
# Shapiro filter
for var in u, v:
var[:] = shapiro2d(var)
# Plot
map2((u[0], v[0]), title='Geostrophic velocity',
quiver_samp=3, xymasked=False, quiver_norm=3, contour=False,
fill=False, figsize=(7, 7), quiver_linewidth=.3, quiver_width=0.003,
quiver_scale=10, right=1, colorbar_shrink=0.8, bottom=0.05, show=False,
savefig=code_file_name(), close=True)
"""Test :func:`~vacumm.misc.grid.regridding.transect`""" # Inits ncfile = "menor.nc" lon0 = 3.31 lat0 = 43.19 lon1 = 4.78 lat1 = 42.01 # Imports from vcmq import DS, data_sample, mixed_layer_depth, N, transect, section2, curve2, code_file_name, os from vacumm.misc.plot import add_map_lines # Read data ds = DS(data_sample(ncfile), 'mars', logger_level='critical') temp = ds.get_temp(squeeze=True) dens = ds.get_dens(squeeze=True) depth = ds.get_depth(squeeze=True) # Compute MLD mld = mixed_layer_depth(dens, depth=depth, mode='deltadens', format_axes=True) del dens # Compute transect tlons = (lon0,lon1) tlats = (lat0,lat1) tlons = N.concatenate([N.linspace(lon0,lon1,100.),N.linspace(lon1,lon1,100.)]) tlats = N.concatenate([N.linspace(lat0,lat1,100.),N.linspace(lat1,lat0,100.)]) xtemp, xlons, xlats = transect(temp, tlons, tlats, getcoords=True, outaxis='dist') xdepth = transect(depth, tlons, tlats) xmld = transect(mld, tlons, tlats)
def load_model_at_regular_dates(ncpat,
varnames=None,
time=None,
lat=None,
lon=None,
level=None,
depths=None,
modeltype='mars',
nt=50,
dtfile=None,
sort=True,
asdict=False,
logger=None,
**kwargs):
"""Read model output at nearest unique dates with optional linear interpolation
Parameters
----------
ncpat: string or list of strings
varnames: string, strings
Generic var names. If None, all variables that are known from the
:mod:`vacumm.data.cf` module are used.
level: string, None, list of floats, array, tuple of them, dict
Here are some possible values:
- "surf" or "bottom": self explenatory
- None or "3d": No slice, so get all levels with no interpolation.
- A list or array of negative depths: get all levels and
interpolate at these depths.
Variables sliced with "surf" and "bottom" are returned with
an id suffixed with "_surf" or "_bottom".
You can speficy different slicings using a tuple
of depth specifications.
You can specialise slicings of a variable using a dictionary with
the key as the variable name.
See also
--------
:func:`sonat.misc.list_files_from_pattern` for more options
Examples
--------
>>> mdict = load_model_at_regular_dates('myfile.nc', level='surf')
>>> mdict = load_model_at_regular_dates('myfile.nc', level=('surf', 'bottom')
>>> mdict = load_model_at_regular_dates('myfile.nc', varnames=['temp', 'sal'],
level={'temp':('surf', 'bottom'), 'sal':[-50, -10]})
>>> mdict = load_model_at_regular_dates('myfile.nc', varnames=['temp', 'sal'],
level={'temp':('surf', '3d'), 'sal':None}, depths=[-50, -10])
"""
# Logger
kwlog = kwfilter(kwargs, 'logger_')
if logger is None:
logger = get_logger(**kwlog)
logger.debug('Loading model at regular dates')
# Get file list
ncfiles = list_files_from_pattern(ncpat, time, dtfile=dtfile, sort=True)
if not ncfiles:
raise SONATError('No file found')
# Time interval
reqtime = time
if time is None:
# First
taxis = ncget_time(ncfiles[0])
if taxis is None:
raise SONATError("Can't get time axis for: " + ncfiles[0])
ctimes = taxis.asComponentTime()
ct0 = ctimes[0]
# Last
if ncfiles[0] != ncfiles[-1]:
taxis = ncget_time(ncfiles[-1])
if taxis is None:
raise SONATError("Can't get time axis for: " + ncfiles[-1])
ctimes = taxis.asComponentTime()
ct1 = ctimes[-1]
# Time
time = (ct0, ct1)
# Generate dates
dates = lindates(time[0], time[1], nt)
# Get time indices
iidict, iiinfo = ncfiles_time_indices(ncfiles,
dates,
getinfo=True,
asslices=True)
if iiinfo['missed'] or iiinfo['duplicates']:
msg = ("You must provide at least {nt} model time steps to read "
"independant dates")
if reqtime:
msg = msg + (", and your requested time range must be enclosed "
"by model time range.")
raise SONATError(msg)
# Read
single = isinstance(varnames, basestring)
if single:
varnames = [varnames]
out = OrderedDict()
vlevels = {}
if not isinstance(level, dict):
level = {'__default__': level}
for ncfile, tslices in iidict.items():
# Dataset instance
ds = DS(ncfile,
modeltype,
logger_name='SONAT.Dataset',
logger_level='error')
# List of well known variables
if varnames is None:
varnames = []
for ncvarname in ds.get_variable_names():
varname = match_known_var(ds[0][ncvarname])
if varname:
varnames.append(varname)
# Loop on variables
vardepth = None
kwvar = dict(lat=lat, lon=lon, verbose=False, bestestimate=False)
for vname in list(varnames):
# Level selector for this variable
if vname in vlevels: # cached
vlevel = vlevels[vname]
else:
vlevel = interpret_level(dicttree_get(level, vname),
astuple=True)
vlevels[vname] = vlevel # cache it
# Loop on level specs
for vlev in vlevel:
# Output vname and vlev check
if not isinstance(vlev, basestring):
vnameo = vname
elif vlev not in ('surf', "bottom", "3d"):
raise SONATError('Depth string must one of '
'surf, bottom, 3d')
elif vlev != '3d':
vnameo = vname + '_' + vlev
else:
vlev = None
vnameo = vname
# Slicing level and output depths
if vlev not in ['surf', 'bottom']:
# numeric so interpolation
if vlev is None:
vdep = depths if depths is not None else None
else:
vdep = vlev
interp = vdep is not None
if interp:
vlev = None
else:
interp = False
# Read and aggregate
vout = out.setdefault(vnameo, [])
# vinterp = None
for tslice in tslices:
# Get var
kwvar['time'] = tslice
var = ds(vname, level=vlev, **kwvar)
# Interpolate at numeric depths
if interp and var.getLevel() is not None:
# Get depths
if True or vardepth is None: #FIXME: bad to always read it
vardepth = ds.get_depth(level=vlev,
zerolid=True,
**kwvar)
# Interpolate
var = ds._interp_at_depths_(var,
vardepth,
vdep,
extrap='top')
# Id with suffix
var.id = vnameo
# Store results
vout.append(var)
# Concatenate
for vname, vout in out.items():
out[vname] = MV2_concatenate(vout)
# Dict
if asdict:
return out
# Single
out = out.values()
if single:
return out[0]
return out
"""Test :meth:`~vacumm.data.misc.dataset.Dataset.get_var` on multiple files and time selections"""
# Inits
ncfiles = "mars2d.xyt.*.nc"
# Imports
from vcmq import DS, os, map2, data_sample
# Glob pattern
result = []
ds = DS(data_sample("mars2d.xyt.*.nc"), 'mars', logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
assert ds.get_ssh().shape == (4, 50, 50)
assert ds.get_ssh(time=("2008-08-15 06", "2008-08-15 07", 'co'),squeeze=True).shape==(50, 50)
# With dates
ds = DS(data_sample("mars2d.xyt.%Y%m%d%H.nc"), 'mars', logger_level='critical',
time=("2008-08-15 06", "2008-08-15 09"))
assert ds.get_ssh(
time=("2008-08-15 06", "2008-08-15 07", 'cc')).shape==(2, 50, 50)
# if re.match(r'[\(\[].*', arg): # classic selector
# return tuple(eval(arg))
if RE_MATCH_TIME(arg) and not arg.isdigit(): # date
return arg
if re.match('[\w\s]*:[\w\s]*(:[\w\s]*)?$', arg): # args to slice
return slice(*[(None if a=='' else eval(a)) for a in arg.split(':')])
arg = eval(arg)
if isinstance(arg, int): # slice at a single index
return slice(arg, (arg+1) if arg!=-1 else None)
if isinstance(arg, float): # selection of a single position
return (arg, arg, 'cob')
return arg
# Open reader or file
if args.generic:
f = DS(args.ncfile, args.generic, logger_level='info' if args.verbose else 'error')
else:
f = cdms2.open(args.ncfile)
# Find a variable name if not provided
if not args.var:
if args.generic:
allvars = f.dataset[0].listvariables()
else:
allvars = f.listvariables()
for var in allvars:
if 'bounds' not in var:
if args.generic:
var = '+'+var
args.var = [var]
break
"""Test :meth:`~vacumm.data.misc.OceanDataset.plot_transect` with MENOR"""
# Inits
ncfile = "menor.nc"
lons = (3.76, 4.7)
lats = (43.1, 42)
# Imports
from vcmq import DS, data_sample, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
# Plot transect
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
ds.plot_transect('temp',
lons,
lats,
figsize=(6, 4),
fill='contourf',
nmax=30,
savefig=figfile,
top=0.9,
right=0.89,
show=False,
close=True)
"""Test :meth:`~vacumm.data.misc.OceanDataset.plot_transect` with MENOR"""
# Inits
ncfile = "menor.nc"
lons = (3.76, 4.7)
lats = (43.1, 42)
# Imports
from vcmq import DS, data_sample, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
# Plot transect
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
ds.plot_transect('temp', lons, lats, figsize=(6,4), fill='contourf', nmax=30,
savefig=figfile, top=0.9, right=0.89, show=False, close=True)
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_depth` in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', logger_level='critical')
depth = ds.get_depth(squeeze=True)
# Plot midlevel
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(depth[depth.shape[0]/2], savefig=figfile, close=True, vmax=0, show=False,
colorbar_shrink=0.6, title='Testing Dataset.get_depth()')
# For unittest
result = [
('files', figfile),
]
"""Test :func:`~vacumm.misc.grid.regridding.transect`"""
# Inits
ncfile = "menor.nc"
lon0 = 3.31
lat0 = 43.19
lon1 = 4.78
lat1 = 42.01
# Imports
from vcmq import DS, data_sample, mixed_layer_depth, N, transect, section2, curve2, code_file_name, os
from vacumm.misc.plot import add_map_lines
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
temp = ds.get_temp(squeeze=True)
dens = ds.get_dens(squeeze=True, potential=True)
depth = ds.get_depth(squeeze=True)
# Compute MLD
mld = mixed_layer_depth(dens, depth=depth, mode='deltadens', format_axes=True)
del dens
# Compute transect
tlons = (lon0, lon1)
tlats = (lat0, lat1)
tlons = N.concatenate(
[N.linspace(lon0, lon1, 100.),
N.linspace(lon1, lon1, 100.)])
tlats = N.concatenate(
[N.linspace(lat0, lat1, 100.),
"""Test the asvar keyword of :meth:`~vacumm.data.misc.dataset.Dataset.finalize_object` on MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, data_sample
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
temp = ds.get_temp()
bathy = ds.get_bathy(asvar=temp)
# For unittest
result = {'assertTupleEqual': [bathy.shape, temp.shape]}
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_temp` on MFS"""
# Inits
ncfile = "mfs.nc"
# Imports
from vcmq import DS, data_sample
# Read data
ds = DS(data_sample(ncfile), 'nemo', logger_level='critical')
temp = ds.get_temp()
lon = temp.getLongitude()
# For unittest
result = {'assertIsNotNone':lon}
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_dens` in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
dens = ds.get_dens(squeeze=True)
# Plot surface density
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(dens[-1], savefig=figfile, close=True, vmin=1025.,show=False)
# For unittest
result = {'files':figfile}
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""Exploitation generique de donnes grilles (:mod:`vacumm.data.misc.dataset`)"""
from vcmq import DS, data_sample, map2
# Initialisation
ds = DS(data_sample('menor.nc'), 'mars', lon=(4, 5), lat=(42.5, 43.5), log_level='debug')
print ds.dataset
# Logging
ds.info('Pratique') # -> ESSAYER WARNING
ds.set_loglevel('debug')
# Coordonnees
lon = ds.get_lon() # -> ESSAYER AU POINT U
grid = ds.get_grid()
# Variables
temp = ds.get_temp(level=slice(-1, None), squeeze=True)
sst = ds.get_sst(squeeze=True) # -> VERIFIER ATTRIBUTS
ds.info('Plot SST')
map2(sst)
sal = ds.get_sal(lon=(4., 4.5))
print temp.shape, sal.shape
# Generique
ds2 = DS(data_sample('mfs.nc'), 'nemo', lon=(4, 5), lat=(42.5, 43.5))
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_depth` in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', logger_level='critical')
depth = ds.get_depth(squeeze=True)
# Plot midlevel
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(depth[depth.shape[0] / 2],
savefig=figfile,
close=True,
vmax=0,
show=False,
colorbar_shrink=0.6,
title='Testing Dataset.get_depth()')
# For unittest
result = [
('files', figfile),
]
"""Test :meth:`~vacumm.data.misc.dataset.Dataset.plot_transect` on MFS"""
# Inits
ncfile = "mfs.nc"
lons = (3.125, 5.5)
lats = (43.4375, 42.125)
# Imports
from vcmq import DS, data_sample, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), 'nemo', logger_level='critical')
# Plot transect
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
ds.plot_transect('temp',
lons,
lats,
outaxis='dist',
show=False,
fill='contourf',
figsize=(6, 4),
savefig=figfile,
top=0.9,
right=0.89,
close=True)
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_variable` with level as a string"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ncfile = data_sample(ncfile)
ds = DS(ncfile, 'mars', logger_level='critical')
tbot = ds.get_temp(level='bottom', squeeze=True)
tsurf = ds.get_temp(level='surf', squeeze=True)
# Plot bottom
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
kw = dict(contour=True, fill='contourf', colorbar_shrink=0.8,
cmap='cmocean_thermal', linewidth=.3)
m = map2(tsurf, subplot=211, close=False, show=False, figsize=(5, 7),
title='Testing Dataset.get_temp(level="surf")', **kw)
map2(tbot, subplot=212, close=True, show=True, m=m,
title='Testing Dataset.get_temp(level="bottom")',
savefig=figfile, **kw)
"""Test :meth:`~vacumm.data.misc.OceanDataset.plot_hsection` with MENOR"""
# Inits
ncfile = "menor.nc"
depth = -1000.
# Imports
from vcmq import DS, data_sample, os, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
# Plot hsection
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
ds.plot_hsection('temp', depth, savefig=figfile, fill='contourf', show=False, close=True)
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_temp` with ``at`` keyword and :meth:`~vacumm.data.misc.dataset.OceanDataset.get_temp_u`"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, data_sample
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
uu = ds.get_u3d()
uv1 = ds.get_u3d(at='v')
uv2 = ds.get_u3d_v()
# For unittest
result = [
('assertNotEqual', [uu.mean(), uv1.mean()]),
('assertEqual', [uv1.mean(), uv2.mean()]),
('assertEqual', [uv1.id, "u3d_v"]),
('assertEqual', [uv2.id, "u3d_v"]),
]
"""Test the asvar keyword of :meth:`~vacumm.data.misc.dataset.Dataset.finalize_object` on MFS"""
# Inits
ncfile = "mfs.nc"
# Imports
from vcmq import DS, data_sample
# Read data
ds = DS(data_sample(ncfile), 'nemo', logger_level='critical')
temp = ds.get_temp()
depth = ds.get_depth(asvar=temp)
# For unittest
result = {'assertTupleEqual':[depth.shape, temp.shape]}
"""Test :meth:`~vacumm.data.misc.OceanDataset.plot_hsection` with MFS"""
# Inits
ncfile = "mfs.nc"
depth = -1000.0
# Imports
from vcmq import DS, data_sample, os, code_file_name
# Setup dataset
ds = DS(data_sample(ncfile), "nemo", logger_level="critical")
# Plot hsection
figfile = code_file_name(ext="png")
if os.path.exists(figfile):
os.remove(figfile)
ds.plot_hsection("temp", depth, savefig=figfile, fill="contourf", show=False, close=True)
"""Test :meth:`~vacumm.data.misc.dataset.OceanDataset.get_mld` with deltadens in MENOR"""
# Inits
ncfile = "menor.nc"
# Imports
from vcmq import DS, os, map2, data_sample, code_file_name
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
mld = ds.get_mld(mode='deltadens', deltadens=0.06, squeeze=True)
# Plot surface density
figfile = code_file_name(ext='png')
if os.path.exists(figfile): os.remove(figfile)
map2(mld, savefig=figfile, close=True, show=False, fill='pcolormesh',
cmap='vacumm_previmer', contour=False)
# For unittest
result = {'files':figfile}
except:
parser.error('--%s: wrong argument' % selname)
select[selname] = val
# Imports
from vcmq import DS, map2, MV2, data_sample
# The file
ncfile = options.ncfile
if not os.path.exists(ncfile):
ncfile = data_sample(ncfile)
if not os.path.exists(ncfile):
parser.error('File not found: ' + ncfile)
# Read temperature and depth
ds = DS(ncfile, options.model, **select)
mld = ds.get_mld(mode='deltatemp', squeeze=1)
# Time average (if needed)
if mld.ndim == 3:
mld = MV2.average(mld, axis=0)
# Plot
map2(mld,
proj='merc',
figsize=(6, 6),
autoresize=0,
title=options.title,
colorbar_shrink=0.7,
right=1,
show=options.disp,
"""Test the asvar keyword of :meth:`~vacumm.data.misc.dataset.Dataset.finalize_object` on MENOR"""
# Inits
ncfile="menor.nc"
# Imports
from vcmq import DS, data_sample
# Read data
ds = DS(data_sample(ncfile), 'mars', logger_level='critical')
temp = ds.get_temp()
bathy = ds.get_bathy(asvar=temp)
# For unittest
result = {'assertTupleEqual':[bathy.shape, temp.shape]}