def test_self_eof (self):
var = self.var
eof, eig, pc = EOF(var,num=1)
netcdf.save("eof_test.nc", [eof,eig,pc])
std = (var - eof*eig*pc).stdev()
rms = (var**2).mean()
self.assertLess(std, rms*1E-3)
def test_io():
from pygeode.formats import netcdf as nc
from pygeode.timeaxis import StandardTime
from pygeode.axis import Pres
from pygeode.dataset import Dataset
import numpy as np
tm = StandardTime(values=np.arange(365), units='days', startdate={'year':2001})
p = Pres(np.arange(100.))
v = (tm * p).rename('v')
# Save the dataset, then reload it immediately
before = Dataset([v])
nc.save('issue004_test.nc', before)
after = nc.open('issue004_test.nc')
# Compare all vars/axes/attributes
for var in before:
assert var.name in after, "Can't find var '%s'"%var.name
var2 = getattr(after,var.name)
assert var2.atts == var.atts, "mismatched metadata. Input: %s, Output %s"%(var.atts,var2.atts)
for axis in before.axes:
axis2 = [a for a in after.axes if a.name == axis.name]
assert len(axis2) == 1, "can't find axis '%s'"%axis.name
axis2 = axis2[0]
# assert axis2.atts == axis.atts, "mismatched metadata. Input: %s, Output %s"%(axis.atts,axis2.atts)
for attname in axis.atts.keys():
assert attname in axis2.atts, "attribute '%s' not found"%attname
assert axis.atts[attname] == axis2.atts[attname], "attribute '%s' changed from '%s' to '%s'"%(attname, axis.atts[attname], axis2.atts[attname])
assert type(axis2) == type(axis), "mismatched axis types. Input: %s, Output %s"%(type(axis), type(axis2))
def test_self_eof(self):
var = self.var
eof, eig, pc = EOF(var, num=1)
netcdf.save("eof_test.nc", [eof, eig, pc])
std = (var - eof * eig * pc).stdev()
rms = (var**2).mean()
self.assertLess(std, rms * 1E-3)
def test_io():
from pygeode.formats import netcdf as nc
from pygeode.timeaxis import StandardTime
from pygeode.axis import Pres
from pygeode.dataset import Dataset
import numpy as np
tm = StandardTime(values=np.arange(365), units='days', startdate={'year':2001})
p = Pres(np.arange(100.))
v = (tm * p).rename('v')
# Save the dataset, then reload it immediately
before = Dataset([v])
nc.save('issue004_test.nc', before)
after = nc.open('issue004_test.nc')
# Compare all vars/axes/attributes
for var in before:
assert var.name in after, "Can't find var '%s'"%var.name
var2 = getattr(after,var.name)
assert var2.atts == var.atts, "mismatched metadata. Input: %s, Output %s"%(var.atts,var2.atts)
for axis in before.axes:
axis2 = [a for a in after.axes if a.name == axis.name]
assert len(axis2) == 1, "can't find axis '%s'"%axis.name
axis2 = axis2[0]
# assert axis2.atts == axis.atts, "mismatched metadata. Input: %s, Output %s"%(axis.atts,axis2.atts)
for attname in list(axis.atts.keys()):
assert attname in axis2.atts, "attribute '%s' not found"%attname
assert axis.atts[attname] == axis2.atts[attname], "attribute '%s' changed from '%s' to '%s'"%(attname, axis.atts[attname], axis2.atts[attname])
assert type(axis2) == type(axis), "mismatched axis types. Input: %s, Output %s"%(type(axis), type(axis2))
def test_opener():
from pygeode.formats import netcdf
from pygeode.tutorial import t1
from pygeode.formats.multifile import openall
netcdf.save("issue090.data", t1)
my_opener = lambda filename: netcdf.open(filename)
f = openall("issue090.d???", opener=my_opener)
def test_opener():
from pygeode.formats import netcdf
from pygeode.tutorial import t1
from pygeode.formats.multifile import openall
netcdf.save("issue090.data", t1)
my_opener = lambda filename: netcdf.open(filename)
f = openall("issue090.d???", opener=my_opener)
def test_encode_decode():
from pygeode.formats import netcdf
import numpy as np
x = make_var()
netcdf.save("issue068_test.nc", x)
y = netcdf.open("issue068_test.nc").dummy
type1 = type(x.station)
type2 = type(y.station)
assert type1 is type2, (type1, type2)
assert x.station == y.station
assert np.all(x.get() == y.get())
def test_encode_decode():
from pygeode.formats import netcdf
import numpy as np
x = make_var()
netcdf.save("issue068_test.nc", x)
y = netcdf.open("issue068_test.nc").dummy
type1 = type(x.station)
type2 = type(y.station)
assert type1 is type2, (type1, type2)
assert x.station == y.station
assert np.all(x.get() == y.get())
def test_issue025():
lat = Lat([80,70,60])
var = Var(axes=[lat], values=[1,2,3], name='2B')
# Save the variable
nc.save ("issue025_test.nc", var)
# This may crash in some versions of the netcdf library.
# Even if it doesn't crash, it's a good idea to enforce the legal
# netcdf names
f = nc.open("issue025_test.nc")
assert len(f.vars) == 1
# Must not start with a digit (should have been filtered)
assert not f.vars[0].name[0].isdigit()
def test_issue015():
from pygeode.formats import netcdf as nc
from pygeode.axis import Lat, Lon, Pres
# Create a simple variable
lat = Lat([75,85,95])
lon = Lon([100, 110, 120, 130])
pres = Pres([1000,900,800,700])
x = (lat-80)**2 + lon - pres/2.
x.name = "stuff"
# Save as a netcdf file
nc.save("issue015_test.nc", x)
# Reload
f = nc.open("issue015_test.nc")
y = f.stuff.load()
def test_issue005():
from pygeode.timeaxis import ModelTime365
from pygeode.axis import TAxis
import numpy as np
from pygeode.var import Var
from pygeode.formats import netcdf as nc
from pygeode import timeutils
# Make a time axis starting at year 0
startdate = dict(year=0,month=1,day=1)
taxis = ModelTime365(values=10200, startdate=startdate, units='days')
# Make some dummy variable
np.random.seed(len(taxis))
values = np.random.randn(len(taxis))
var = Var(axes=[taxis], values=values, name='x')
# Save it
nc.save("issue005_test.nc", var)
# Load it
f = nc.open("issue005_test.nc")
# Make sure we have a regular time axis
# (no climatologies!)
assert f.time.__class__ == ModelTime365
assert hasattr(f.time,'year')
# Okay, now reload it, but override the axis coming in
f = nc.open("issue005_test.nc", dimtypes=dict(time=TAxis(taxis.values)))
# Make sure we dimtypes is still working properly
assert f.x.axes[0].__class__ == TAxis
# For good measure, test that climatologies are still produced
taxis = timeutils.modify(taxis,exclude='year',uniquify=True)
values = np.random.randn(len(taxis))
var = Var(axes=[taxis], values=values, name='c')
nc.save("issue005_test.nc", var)
f = nc.open("issue005_test.nc")
assert not hasattr(f.time,'year')
def test_issue005():
from pygeode.timeaxis import ModelTime365
from pygeode.axis import TAxis
import numpy as np
from pygeode.var import Var
from pygeode.formats import netcdf as nc
from pygeode import timeutils
# Make a time axis starting at year 0
startdate = dict(year=0, month=1, day=1)
taxis = ModelTime365(values=10200, startdate=startdate, units='days')
# Make some dummy variable
np.random.seed(len(taxis))
values = np.random.randn(len(taxis))
var = Var(axes=[taxis], values=values, name='x')
# Save it
nc.save("issue005_test.nc", var)
# Load it
f = nc.open("issue005_test.nc")
# Make sure we have a regular time axis
# (no climatologies!)
assert f.time.__class__ == ModelTime365
assert hasattr(f.time, 'year')
# Okay, now reload it, but override the axis coming in
f = nc.open("issue005_test.nc", dimtypes=dict(time=TAxis(taxis.values)))
# Make sure we dimtypes is still working properly
assert f.x.axes[0].__class__ == TAxis
# For good measure, test that climatologies are still produced
taxis = timeutils.modify(taxis, exclude='year', uniquify=True)
values = np.random.randn(len(taxis))
var = Var(axes=[taxis], values=values, name='c')
nc.save("issue005_test.nc", var)
f = nc.open("issue005_test.nc")
assert not hasattr(f.time, 'year')
# Issue 22 - plot attributes get overridden by NamedAxis defaults
# https://github.com/pygeode/pygeode/issues/22
# Make a sample file with a non-annotated pressure axis
from pygeode.axis import NamedAxis, Pres
from pygeode.formats import netcdf as nc
lat = NamedAxis(values=[-80,-70,-60,-50], name='lat')
p1 = NamedAxis(values=[1000.,900.,800.], name='p1')
x = lat * p1
x.name = 'x'
nc.save("issue022_test.nc", x)
# Load it back in
d = nc.open("issue022_test.nc", dimtypes={'p1':Pres})
# plotatts should be from the new (dimtypes) axis, not copied from the old one?
# (also implicitly asserts that other metadata (such as the name) are still
# copied from the old axis)
assert d.p1.plotatts == Pres.plotatts
import pygeode as pyg
import numpy as np
import pylab as pyl
from pygeode.formats import netcdf as nc
lat = pyg.gausslat(32)
lon = pyg.Lon(np.arange(0, 360, 360 / 64.))
ln_grid, lt_grid = np.meshgrid(lon.values, lat.values)
T_values = 260. + 40 * np.exp(-(lt_grid / 45.)**2) + 0.05 * lt_grid * np.sin(
3 * ln_grid * np.pi / 180.)
T_c = 260. + 40 * np.exp(-(lt_grid / 45.)**2)
T_wave = 0.05 * lt_grid * np.sin(3 * ln_grid * np.pi / 180.)
T = pyg.Var((lat, lon), name='Temp', values=T_c + T_wave, atts={'units': 'K'})
d = pyg.Dataset(
[T], atts={'history': 'Synthetic Temperature data generated by pygeode'})
nc.save('t_sample.nc', d)
def test_self_svd(self):
var1 = self.var1
eof1, pc1, eof2, pc2 = SVD(var1, var1, num=1, subspace=1)
netcdf.save("svd_test.nc", [eof1, pc1, eof2, pc2])
self.assertTrue(np.allclose(eof1.get(), eof2.get()))
self.assertTrue(np.allclose(pc1.get(), pc2.get()))
# Issue 22 - plot attributes get overridden by NamedAxis defaults
# https://github.com/pygeode/pygeode/issues/22
# Make a sample file with a non-annotated pressure axis
from pygeode.axis import NamedAxis, Pres
from pygeode.formats import netcdf as nc
lat = NamedAxis(values=[-80, -70, -60, -50], name='lat')
p1 = NamedAxis(values=[1000., 900., 800.], name='p1')
x = lat * p1
x.name = 'x'
nc.save("issue022_test.nc", x)
# Load it back in
d = nc.open("issue022_test.nc", dimtypes={'p1': Pres})
# plotatts should be from the new (dimtypes) axis, not copied from the old one?
# (also implicitly asserts that other metadata (such as the name) are still
# copied from the old axis)
assert d.p1.plotatts == Pres.plotatts
def test_self_svd (self):
var1 = self.var1
eof1, pc1, eof2, pc2 = SVD(var1,var1,num=1,subspace=1)
netcdf.save("svd_test.nc", [eof1,pc1,eof2,pc2])
self.assertTrue(np.allclose(eof1.get(),eof2.get()))
self.assertTrue(np.allclose(pc1.get(),pc2.get()))