def __init__(self, **kwargs):
##
## tried making this a sub-class of Field ... but it messed up something in the cfdm.write() methods.
## Something must be keyed on "Field..." .. perhaps on copy of construct ...
##
self.f = cfdm.Field(kwargs)
def test_GATHERING_create(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
# Define the gathered values
gathered_array = numpy.array([[280, 282.5, 281], [279, 278, 277.5]],
dtype='float32')
# Define the list array values
list_array = [1, 4, 5]
# Initialise the list variable
list_variable = cfdm.List(data=cfdm.Data(list_array))
# Initialise the gathered array object
array = cfdm.GatheredArray(
compressed_array=cfdm.Data(gathered_array),
compressed_dimension=1,
shape=(2, 3, 2), size=12, ndim=3,
list_variable=list_variable
)
# Create the field construct with the domain axes and the
# gathered array
tas = cfdm.Field(properties={'standard_name': 'air_temperature',
'units': 'K'})
# Create the domain axis constructs for the uncompressed array
T = tas.set_construct(cfdm.DomainAxis(2))
Y = tas.set_construct(cfdm.DomainAxis(3))
X = tas.set_construct(cfdm.DomainAxis(2))
# Set the data for the field
tas.set_data(cfdm.Data(array), axes=[T, Y, X])
self.assertTrue((tas.data.array == numpy.ma.masked_array(
data=[[[1, 280.0],
[1, 1],
[282.5, 281.0]],
[[1, 279.0],
[1, 1],
[278.0, 277.5]]],
mask=[[[True, False],
[True, True],
[False, False]],
[[True, False],
[True, True],
[False, False]]],
fill_value=1e+20,
dtype='float32')).all())
self.assertEqual(tas.data.get_compression_type(), 'gathered')
self.assertTrue((tas.data.compressed_array == numpy.array(
[[280., 282.5, 281.],
[279., 278., 277.5]], dtype='float32')).all())
self.assertTrue((tas.data.get_list().data.array == numpy.array(
[1, 4, 5])).all())
def test_netCDF_geometry_variable(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field()
f.nc_set_geometry_variable('qwerty')
self.assertTrue(f.nc_has_geometry_variable())
self.assertEqual(f.nc_get_geometry_variable(), 'qwerty')
self.assertEqual(f.nc_get_geometry_variable(default=None), 'qwerty')
self.assertEqual(f.nc_del_geometry_variable(), 'qwerty')
self.assertFalse(f.nc_has_geometry_variable())
self.assertIsNone(f.nc_get_geometry_variable(default=None))
self.assertIsNone(f.nc_del_geometry_variable(default=None))
f.nc_set_geometry_variable('/ncvar')
self.assertEqual(f.nc_get_geometry_variable(), 'ncvar')
f.nc_set_geometry_variable('/ncvar/qwerty')
self.assertEqual(f.nc_get_geometry_variable(), '/ncvar/qwerty')
with self.assertRaises(ValueError):
f.nc_set_geometry_variable('group/ncvar')
with self.assertRaises(ValueError):
f.nc_set_geometry_variable('group/')
with self.assertRaises(ValueError):
f.nc_set_geometry_variable('group/ncvar/')
with self.assertRaises(ValueError):
f.nc_set_geometry_variable('/group/ncvar/')
with self.assertRaises(ValueError):
f.nc_set_geometry_variable('/')
def test_netCDF_variable_groups(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field()
f.nc_set_variable('ncdim')
with self.assertRaises(ValueError):
f.nc_set_variable_groups(['/forecast'])
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
attrs = f.nc_clear_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
f.nc_set_variable_groups(['forecast', 'model'])
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ('forecast', 'model'))
self.assertEqual(f.nc_get_variable(), '/forecast/model/ncdim')
attrs = f.nc_clear_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ('forecast', 'model'))
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
self.assertEqual(f.nc_get_variable(), 'ncdim')
f.nc_set_variable('ncdim')
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ())
f.nc_set_variable('/ncdim')
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
f.nc_set_variable('/forecast/model/ncdim')
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ('forecast', 'model'))
f.nc_del_variable()
attrs = f.nc_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
with self.assertRaises(ValueError):
f.nc_set_variable_groups(['forecast', 'model'])
def test_netCDF_geometry_variable_groups(self):
"""Test geometry variable groups access NetCDF methods."""
f = cfdm.Field()
f.nc_set_geometry_variable("ncvar")
with self.assertRaises(ValueError):
f.nc_set_geometry_variable_groups(["/forecast"])
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
attrs = f.nc_clear_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
f.nc_set_geometry_variable_groups(["forecast", "model"])
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ("forecast", "model"))
self.assertEqual(f.nc_get_geometry_variable(), "/forecast/model/ncvar")
attrs = f.nc_clear_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ("forecast", "model"))
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
self.assertEqual(f.nc_get_geometry_variable(), "ncvar")
f.nc_set_geometry_variable("ncvar")
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ())
f.nc_set_geometry_variable("/ncvar")
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
f.nc_set_geometry_variable("/forecast/model/ncvar")
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertEqual(attrs, ("forecast", "model"))
f.nc_del_geometry_variable()
attrs = f.nc_geometry_variable_groups()
self.assertIsInstance(attrs, tuple)
self.assertFalse(attrs)
with self.assertRaises(ValueError):
f.nc_set_geometry_variable_groups(["forecast", "model"])
def test_DSG_contiguous(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = self.c.copy()
self.assertEqual(len(f), 2)
# Select the specific humidity field
q = [g for g in f
if g.get_property('standard_name') == 'specific_humidity'][0]
self.assertTrue(q._equals(self.a, q.data.array))
cfdm.write(f, tempfile)
g = cfdm.read(tempfile)
self.assertEqual(len(g), len(f))
for i in range(len(f)):
self.assertTrue(g[i].equals(f[i], verbose=3))
# ------------------------------------------------------------
# Test creation
# ------------------------------------------------------------
# Define the ragged array values
ragged_array = numpy.array([280, 282.5, 281, 279, 278, 279.5],
dtype='float32')
# Define the count array values
count_array = [2, 4]
# Create the count variable
count_variable = cfdm.Count(data=cfdm.Data(count_array))
count_variable.set_property('long_name',
'number of obs for this timeseries')
# Create the contiguous ragged array object
array = cfdm.RaggedContiguousArray(
compressed_array=cfdm.NumpyArray(ragged_array),
shape=(2, 4), size=8, ndim=2,
count_variable=count_variable)
# Create the field construct with the domain axes and the ragged
# array
tas = cfdm.Field()
tas.set_properties({'standard_name': 'air_temperature',
'units': 'K',
'featureType': 'timeSeries'})
# Create the domain axis constructs for the uncompressed array
X = tas.set_construct(cfdm.DomainAxis(4))
Y = tas.set_construct(cfdm.DomainAxis(2))
# Set the data for the field
tas.set_data(cfdm.Data(array), axes=[Y, X])
cfdm.write(tas, tempfile)
def test_GATHERING_create(self):
"""Test the creation of a construct with a gathered array."""
# Define the gathered values
gathered_array = numpy.array([[280, 282.5, 281], [279, 278, 277.5]],
dtype="float32")
# Define the list array values
list_array = [1, 4, 5]
# Initialise the list variable
list_variable = cfdm.List(data=cfdm.Data(list_array))
# Initialise the gathered array object
array = cfdm.GatheredArray(
compressed_array=cfdm.Data(gathered_array),
compressed_dimension=1,
shape=(2, 3, 2),
size=12,
ndim=3,
list_variable=list_variable,
)
# Create the field construct with the domain axes and the
# gathered array
tas = cfdm.Field(properties={
"standard_name": "air_temperature",
"units": "K"
})
# Create the domain axis constructs for the uncompressed array
T = tas.set_construct(cfdm.DomainAxis(2))
Y = tas.set_construct(cfdm.DomainAxis(3))
X = tas.set_construct(cfdm.DomainAxis(2))
# Set the data for the field
tas.set_data(cfdm.Data(array), axes=[T, Y, X])
self.assertTrue((tas.data.array == numpy.ma.masked_array(
data=[
[[1, 280.0], [1, 1], [282.5, 281.0]],
[[1, 279.0], [1, 1], [278.0, 277.5]],
],
mask=[
[[True, False], [True, True], [False, False]],
[[True, False], [True, True], [False, False]],
],
fill_value=1e20,
dtype="float32",
)).all())
self.assertEqual(tas.data.get_compression_type(), "gathered")
self.assertTrue((tas.data.compressed_array == numpy.array(
[[280.0, 282.5, 281.0], [279.0, 278.0, 277.5]],
dtype="float32",
)).all())
self.assertTrue(
(tas.data.get_list().data.array == numpy.array([1, 4, 5])).all())
def test_netCDF_group_attributes(self):
"""Test group attributes access and (un)setting methods."""
f = cfdm.Field()
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
attrs = f.nc_clear_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
f.nc_set_group_attributes({"comment": "somthing"})
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {"comment": "somthing"})
attrs = f.nc_clear_group_attributes()
self.assertEqual(attrs, {"comment": "somthing"})
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
f.nc_set_group_attributes({"comment": "something"})
f.nc_set_group_attributes({"foo": "bar"})
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {"comment": "something", "foo": "bar"})
f.nc_clear_group_attributes()
f.nc_set_group_attribute("foo", "bar")
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {"foo": "bar"})
f.nc_set_group_attribute("foo", "bar2")
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {"foo": "bar2"})
f.set_properties({"prop1": "value1", "comment": "variable comment"})
f.nc_clear_group_attributes()
f.nc_set_group_attributes({"comment": None, "foo": "bar"})
self.assertEqual(
f.nc_group_attributes(values=True),
{
"comment": "variable comment",
"foo": "bar"
},
)
def test_netCDF_group_attributes(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field()
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
attrs = f.nc_clear_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
f.nc_set_group_attributes({'comment': 'somthing'})
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {'comment': 'somthing'})
attrs = f.nc_clear_group_attributes()
self.assertEqual(attrs, {'comment': 'somthing'})
attrs = f.nc_group_attributes()
self.assertIsInstance(attrs, dict)
self.assertFalse(attrs)
f.nc_set_group_attributes({'comment': 'something'})
f.nc_set_group_attributes({'foo': 'bar'})
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {'comment': 'something', 'foo': 'bar'})
f.nc_clear_group_attributes()
f.nc_set_group_attribute('foo', 'bar')
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {'foo': 'bar'})
f.nc_set_group_attribute('foo', 'bar2')
attrs = f.nc_group_attributes()
self.assertEqual(attrs, {'foo': 'bar2'})
f.set_properties({'prop1': 'value1',
'comment': 'variable comment'})
f.nc_clear_group_attributes()
f.nc_set_group_attributes({'comment': None,
'foo': 'bar'})
self.assertEqual(f.nc_group_attributes(values=True),
{'comment': 'variable comment',
'foo': 'bar'})
def test_netCDF_geometry_variable(self):
"""Test geometry variable access and (un)setting methods."""
f = cfdm.Field()
f.nc_set_geometry_variable("qwerty")
self.assertTrue(f.nc_has_geometry_variable())
self.assertEqual(f.nc_get_geometry_variable(), "qwerty")
self.assertEqual(f.nc_get_geometry_variable(default=None), "qwerty")
self.assertEqual(f.nc_del_geometry_variable(), "qwerty")
self.assertFalse(f.nc_has_geometry_variable())
self.assertIsNone(f.nc_get_geometry_variable(default=None))
self.assertIsNone(f.nc_del_geometry_variable(default=None))
f.nc_set_geometry_variable("/ncvar")
self.assertEqual(f.nc_get_geometry_variable(), "ncvar")
f.nc_set_geometry_variable("/ncvar/qwerty")
self.assertEqual(f.nc_get_geometry_variable(), "/ncvar/qwerty")
for nc_var_name in self.nc_grouped_variable_names:
with self.assertRaises(ValueError):
f.nc_set_geometry_variable(nc_var_name)
def test_netCDF_variable_dimension(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field()
f.nc_set_variable('qwerty')
self.assertTrue(f.nc_has_variable())
self.assertTrue(f.nc_get_variable() == 'qwerty')
self.assertTrue(f.nc_get_variable(default=None) == 'qwerty')
self.assertTrue(f.nc_del_variable() == 'qwerty')
self.assertFalse(f.nc_has_variable())
self.assertTrue(f.nc_get_variable(default=None) == None)
self.assertTrue(f.nc_del_variable(default=None) == None)
d = cfdm.DomainAxis()
d.nc_set_dimension('qwerty')
self.assertTrue(d.nc_has_dimension())
self.assertTrue(d.nc_get_dimension() == 'qwerty')
self.assertTrue(d.nc_get_dimension(default=None) == 'qwerty')
self.assertTrue(d.nc_del_dimension() == 'qwerty')
self.assertFalse(d.nc_has_dimension())
self.assertTrue(d.nc_get_dimension(default=None) == None)
self.assertTrue(d.nc_del_dimension(default=None) == None)
d = cfdm.Count()
d.nc_set_sample_dimension('qwerty')
self.assertTrue(d.nc_has_sample_dimension())
self.assertTrue(d.nc_get_sample_dimension() == 'qwerty')
self.assertTrue(d.nc_get_sample_dimension(default=None) == 'qwerty')
self.assertTrue(d.nc_del_sample_dimension() == 'qwerty')
self.assertFalse(d.nc_has_sample_dimension())
self.assertTrue(d.nc_get_sample_dimension(default=None) == None)
self.assertTrue(d.nc_del_sample_dimension(default=None) == None)
import netCDF4
import cfdm
import numpy
f = cfdm.Field(properties={'standard_name': 'precipitation_flux'})
dc = cfdm.DimensionCoordinate(properties={'long_name': 'Longitude'},
data=cfdm.Data([0, 1, 2.]))
fa = cfdm.FieldAncillary(
properties={'standard_name': 'precipitation_flux status_flag'},
data=cfdm.Data(numpy.array([0, 0, 2], dtype='int8')))
longitude_axis = f.set_construct(cfdm.DomainAxis(3))
key = f.set_construct(dc, axes=longitude_axis)
cm = cfdm.CellMethod(axes=longitude_axis, method='minimum')
f.set_construct(cm)
import numpy
import cfdm
# Initialize the field construct
tas = cfdm.Field(properties={
'project': 'research',
'standard_name': 'air_temperature',
'units': 'K'
})
# Create and set domain axis constructs
axis_T = tas.set_construct(cfdm.DomainAxis(1))
axis_Z = tas.set_construct(cfdm.DomainAxis(1))
axis_Y = tas.set_construct(cfdm.DomainAxis(10))
axis_X = tas.set_construct(cfdm.DomainAxis(9))
# Set the field construct data
tas.set_data(cfdm.Data(numpy.arange(90.).reshape(10, 9)),
axes=[axis_Y, axis_X])
# Create and set the cell method constructs
cell_method1 = cfdm.CellMethod(axes=[axis_Y, axis_X],
method='mean',
qualifiers={
'where': 'land',
'interval':
[cfdm.Data(0.1, units='degrees')]
})
cell_method2 = cfdm.CellMethod(axes=axis_T, method='maximum')
def test_netCDF_variable_dimension(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field()
f.nc_set_variable('qwerty')
self.assertTrue(f.nc_has_variable())
self.assertEqual(f.nc_get_variable(), 'qwerty')
self.assertEqual(f.nc_get_variable(default=None), 'qwerty')
self.assertEqual(f.nc_del_variable(), 'qwerty')
self.assertFalse(f.nc_has_variable())
self.assertIsNone(f.nc_get_variable(default=None))
self.assertIsNone(f.nc_del_variable(default=None))
f.nc_set_variable('/ncvar')
self.assertEqual(f.nc_get_variable(), 'ncvar')
f.nc_set_variable('/ncvar/qwerty')
self.assertEqual(f.nc_get_variable(), '/ncvar/qwerty')
with self.assertRaises(ValueError):
f.nc_set_variable(None)
with self.assertRaises(ValueError):
f.nc_set_variable('/')
with self.assertRaises(ValueError):
f.nc_set_variable('group/ncvar')
with self.assertRaises(ValueError):
f.nc_set_variable('group/')
with self.assertRaises(ValueError):
f.nc_set_variable('group/ncvar/')
with self.assertRaises(ValueError):
f.nc_set_variable('/group/ncvar/')
d = cfdm.DomainAxis()
d.nc_set_dimension('qwerty')
self.assertTrue(d.nc_has_dimension())
self.assertEqual(d.nc_get_dimension(), 'qwerty')
self.assertEqual(d.nc_get_dimension(default=None), 'qwerty')
self.assertEqual(d.nc_del_dimension(), 'qwerty')
self.assertFalse(d.nc_has_dimension())
self.assertIsNone(d.nc_get_dimension(default=None))
self.assertIsNone(d.nc_del_dimension(default=None))
d.nc_set_dimension('/ncdim')
self.assertEqual(d.nc_get_dimension(), 'ncdim')
d.nc_set_dimension('/ncdim/qwerty')
self.assertEqual(d.nc_get_dimension(), '/ncdim/qwerty')
with self.assertRaises(ValueError):
d.nc_set_dimension(None)
with self.assertRaises(ValueError):
d.nc_set_dimension('/')
with self.assertRaises(ValueError):
d.nc_set_dimension('group/ncdim')
with self.assertRaises(ValueError):
d.nc_set_dimension('group/')
with self.assertRaises(ValueError):
d.nc_set_dimension('group/ncdim/')
with self.assertRaises(ValueError):
d.nc_set_dimension('/group/ncdim/')
d = cfdm.Count()
d.nc_set_sample_dimension('qwerty')
self.assertTrue(d.nc_has_sample_dimension())
self.assertEqual(d.nc_get_sample_dimension(), 'qwerty')
self.assertEqual(d.nc_get_sample_dimension(default=None), 'qwerty')
self.assertEqual(d.nc_del_sample_dimension(), 'qwerty')
self.assertFalse(d.nc_has_sample_dimension())
self.assertIsNone(d.nc_get_sample_dimension(default=None))
self.assertIsNone(d.nc_del_sample_dimension(default=None))
d.nc_set_sample_dimension('/ncdim')
self.assertEqual(d.nc_get_sample_dimension(), 'ncdim')
d.nc_set_sample_dimension('/ncdim/qwerty')
self.assertEqual(d.nc_get_sample_dimension(), '/ncdim/qwerty')
with self.assertRaises(ValueError):
d.nc_set_sample_dimension(None)
with self.assertRaises(ValueError):
d.nc_set_sample_dimension('/')
with self.assertRaises(ValueError):
d.nc_set_sample_dimension('group/ncdim')
with self.assertRaises(ValueError):
d.nc_set_sample_dimension('group/')
with self.assertRaises(ValueError):
d.nc_set_sample_dimension('group/ncdim/')
with self.assertRaises(ValueError):
d.nc_set_sample_dimension('/group/ncdim/')
# ------------------------------------------------------------
# Global attributes
# ------------------------------------------------------------
# values keyword
f = cfdm.Field()
f.nc_set_global_attribute('Conventions', 'CF-1.8')
f.nc_set_global_attribute('project')
f.nc_set_global_attribute('foo')
f.set_property('Conventions', 'Y')
f.set_property('project', 'X')
self.assertEqual(f.nc_global_attributes(values=True),
{'Conventions': 'CF-1.8',
'project': 'X',
'foo': None})
f = cfdm.Field()
self.assertEqual(f.nc_clear_global_attributes(), {})
f.nc_set_global_attribute('Conventions')
f.nc_set_global_attribute('project', 'X')
self.assertEqual(f.nc_global_attributes(), {'Conventions': None,
'project': 'X'})
f.nc_set_global_attribute('project')
f.nc_set_global_attribute('comment', None)
self.assertEqual(f.nc_global_attributes(), {'Conventions': None,
'project': None,
'comment': None})
self.assertEqual(f.nc_clear_global_attributes(), {'Conventions': None,
'project': None,
'comment': None})
self.assertEqual(f.nc_global_attributes(), {})
f.nc_set_global_attribute('Conventions')
f.nc_set_global_attribute('project')
self.assertEqual(f.nc_global_attributes(), {'Conventions': None,
'project': None})
_ = f.nc_clear_global_attributes()
f.nc_set_global_attributes({})
self.assertEqual(f.nc_global_attributes(), {})
f.nc_set_global_attributes({'comment': 123}, copy=False)
self.assertEqual(f.nc_global_attributes(), {'comment': 123})
f.nc_set_global_attributes({'comment': None, 'foo': 'bar'})
self.assertEqual(f.nc_global_attributes(), {'comment': None,
'foo': 'bar'})
f = cfdm.Field()
f.set_properties({'foo': 'bar', 'comment': 'variable comment'})
f.nc_set_variable('tas')
d = f.set_construct(cfdm.DomainAxis(2))
f.set_data(cfdm.Data([8, 9]), axes=[d])
f2 = f.copy()
f2.nc_set_variable('ua')
cfdm.write([f, f2], tempfile1,
file_descriptors={'comment': 'global comment',
'qwerty': 'asdf'})
g = cfdm.read(tempfile1)
self.assertEqual(len(g), 2)
for x in g:
self.assertEqual(x.properties(), {'comment': 'variable comment',
'foo': 'bar',
'qwerty': 'asdf',
'Conventions': 'CF-'+cfdm.CF()})
self.assertEqual(x.nc_global_attributes(),
{'comment': 'global comment',
'qwerty': None,
'Conventions': None})
cfdm.write(g, tempfile2)
h = cfdm.read(tempfile2)
for x, y in zip(h, g):
self.assertEqual(x.properties(), y.properties())
self.assertEqual(x.nc_global_attributes(),
y.nc_global_attributes())
self.assertTrue(x.equals(y, verbose=3))
self.assertTrue(y.equals(x, verbose=3))
g[1].nc_set_global_attribute('comment', 'different comment')
cfdm.write(g, tempfile3)
h = cfdm.read(tempfile3)
for x, y in zip(h, g):
self.assertEqual(x.properties(), y.properties())
self.assertEqual(x.nc_global_attributes(), {'comment': None,
'qwerty': None,
'Conventions': None})
self.assertTrue(x.equals(y, verbose=3))
self.assertTrue(y.equals(x, verbose=3))
def test_DSG_contiguous(self):
"""TODO DOCS."""
f = self.c.copy()
self.assertEqual(len(f), 2)
# Select the specific humidity field
q = [
g for g in f
if g.get_property("standard_name") == "specific_humidity"
][0]
self.assertTrue(q._equals(self.a, q.data.array))
cfdm.write(f, tempfile)
g = cfdm.read(tempfile)
self.assertEqual(len(g), len(f))
for i in range(len(f)):
self.assertTrue(g[i].equals(f[i], verbose=3))
# ------------------------------------------------------------
# Test creation
# ------------------------------------------------------------
# Define the ragged array values
ragged_array = numpy.array([280, 282.5, 281, 279, 278, 279.5],
dtype="float32")
# Define the count array values
count_array = [2, 4]
# Create the count variable
count_variable = cfdm.Count(data=cfdm.Data(count_array))
count_variable.set_property("long_name",
"number of obs for this timeseries")
# Create the contiguous ragged array object
array = cfdm.RaggedContiguousArray(
compressed_array=cfdm.NumpyArray(ragged_array),
shape=(2, 4),
size=8,
ndim=2,
count_variable=count_variable,
)
# Create the field construct with the domain axes and the ragged
# array
tas = cfdm.Field()
tas.set_properties({
"standard_name": "air_temperature",
"units": "K",
"featureType": "timeSeries",
})
# Create the domain axis constructs for the uncompressed array
X = tas.set_construct(cfdm.DomainAxis(4))
Y = tas.set_construct(cfdm.DomainAxis(2))
# Set the data for the field
tas.set_data(cfdm.Data(array), axes=[Y, X])
cfdm.write(tas, tempfile)
def test_STRING(self):
"""Test constructs with underlying string type arrays."""
for array in (
numpy.ma.array(list("abcdefghij"), dtype="S"),
numpy.ma.array(
["a", "b1", "c12", "d123", "e1234", "f", "g", "h", "i", "j"],
dtype="S",
),
):
# Initialize the field
tas = cfdm.Field(
properties={
"project": "research",
"standard_name": "air_temperature",
"units": "K",
}
)
# Create and set domain axes
tas.set_construct(cfdm.DomainAxis(1))
tas.set_construct(cfdm.DomainAxis(1))
axis_Y = tas.set_construct(cfdm.DomainAxis(10))
axis_X = tas.set_construct(cfdm.DomainAxis(9))
# Set the field data
tas.set_data(
cfdm.Data(numpy.arange(90.0).reshape(10, 9)),
axes=[axis_Y, axis_X],
)
# Create and set the dimension coordinates
dimension_coordinate_Y = cfdm.DimensionCoordinate(
properties={
"standard_name": "grid_latitude",
"units": "degrees",
},
data=cfdm.Data(numpy.arange(10.0)),
bounds=cfdm.Bounds(
data=cfdm.Data(numpy.arange(20).reshape(10, 2))
),
)
dimension_coordinate_X = cfdm.DimensionCoordinate(
properties={
"standard_name": "grid_longitude",
"units": "degrees",
},
data=cfdm.Data(numpy.arange(9.0)),
bounds=cfdm.Bounds(
data=cfdm.Data(numpy.arange(18).reshape(9, 2))
),
)
tas.set_construct(dimension_coordinate_Y, axes=[axis_Y])
tas.set_construct(dimension_coordinate_X, axes=[axis_X])
# Create and set the auxiliary coordinates
array[0] = numpy.ma.masked
aux0 = cfdm.AuxiliaryCoordinate(
properties={"long_name": "Grid latitude name"},
data=cfdm.Data(array),
)
tas.set_construct(aux0, axes=[axis_Y])
cfdm.write(tas, tempfile)
tas1 = cfdm.read(tempfile)[0]
aux1 = tas1.constructs.filter_by_identity(
"long_name=Grid latitude name"
).value()
self.assertEqual(aux0.data.shape, array.shape, aux0.data.shape)
self.assertEqual(aux1.data.shape, array.shape, aux1.data.shape)
print("\n**Field ancillaries**\n")
a = t.get_construct("fieldancillary0")
a
a.properties()
a.data
print("\n**Field creation**\n")
print("\n**Stage 1:** The field construct is created without metadata\n")
print("\n**Stage 2:** Metadata constructs are created independently.\n")
print("\n**Stage 3:** The metadata constructs are inserted into the field\n")
p = cfdm.Field(properties={"standard_name": "precipitation_flux"})
p
dc = cfdm.DimensionCoordinate(properties={"long_name": "Longitude"},
data=cfdm.Data([0, 1, 2.0]))
dc
fa = cfdm.FieldAncillary(
properties={"standard_name": "precipitation_flux status_flag"},
data=cfdm.Data(numpy.array([0, 0, 2], dtype="int8")),
)
fa
p = cfdm.Field()
p
p.set_property("standard_name", "precipitation_flux")
p
dc = cfdm.DimensionCoordinate()
dc
def test_create_field(self):
"""TODO DOCS."""
# Dimension coordinates
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.0)))
dim1.set_property("standard_name", "grid_latitude")
dim1.set_property("units", "degrees")
data = numpy.arange(9.0) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property("standard_name", "grid_longitude")
dim0.set_property("units", "degrees")
dim0.nc_set_variable("x")
array = dim0.data.array
array = numpy.array([array - 0.5, array + 0.5]).transpose((1, 0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim2 = cfdm.DimensionCoordinate(
data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.0]])),
)
dim2.set_property("standard_name",
"atmosphere_hybrid_height_coordinate")
dim2.set_property("computed_standard_name", "altitude")
# Auxiliary coordinates
ak = cfdm.DomainAncillary(data=cfdm.Data([10.0]))
ak.set_property("units", "m")
ak.id = "atmosphere_hybrid_height_coordinate_ak"
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.0]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.0]))
bk.id = "atmosphere_hybrid_height_coordinate_bk"
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.0]])))
aux2 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(-45, 45, dtype="int32").reshape(10, 9)))
aux2.set_property("units", "degree_N")
aux2.set_property("standard_name", "latitude")
aux3 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(60, 150, dtype="int32").reshape(9, 10)))
aux3.set_property("standard_name", "longitude")
aux3.set_property("units", "degreeE")
array = numpy.ma.array(
[
"alpha",
"beta",
"gamma",
"delta",
"epsilon",
"zeta",
"eta",
"theta",
"iota",
"kappa",
],
dtype="S",
)
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property("long_name", "greek_letters")
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1 + numpy.arange(90.0).reshape(9, 10) * 1234))
msr0.set_measure("area")
msr0.set_property("units", "km2")
msr0.nc_set_variable("areacella")
# Data
data = cfdm.Data(numpy.arange(90.0).reshape(10, 9))
properties = {"units": "m s-1"}
f = cfdm.Field(properties=properties)
f.set_property("standard_name", "eastward_wind")
da = cfdm.DomainAxis(9)
da.nc_set_dimension("grid_longitude")
axisX = f.set_construct(da)
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=axisX)
y = f.set_construct(dim1, axes=axisY)
z = f.set_construct(dim2, axes=[axisZ])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=axisZ)
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
"grid_mapping_name": "rotated_latitude_longitude",
"grid_north_pole_latitude": 38.0,
"grid_north_pole_longitude": 190.0,
})
datum = cfdm.Datum(parameters={"earth_radius": 6371007})
ref0 = cfdm.CoordinateReference(
coordinate_conversion=coordinate_conversion,
datum=datum,
coordinates=[x, y, lat, lon],
)
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property("standard_name", "surface_altitude")
orog.set_property("units", "m")
orog = f.set_construct(orog, axes=[axisY, axisX])
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
"standard_name": "atmosphere_hybrid_height_coordinate",
"computed_standard_name": "altitude",
},
domain_ancillaries={
"orog": orog,
"a": ak,
"b": bk
},
)
ref1 = cfdm.CoordinateReference(
coordinates=[z],
datum=datum,
coordinate_conversion=coordinate_conversion,
)
ref1 = f.set_construct(ref1)
# Field ancillary variables
g = f.copy()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property("standard_name", "ancillaryA")
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property("long_name", "ancillaryB")
f.set_construct(anc, axes=axisX)
g = f[..., 0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property("foo", "bar")
f.set_construct(anc, axes=[axisY])
f.set_property("flag_values", numpy.array([1, 2, 4], "int32"))
f.set_property("flag_meanings", "a bb ccc")
f.set_property("flag_masks", [2, 1, 0])
cm0 = cfdm.CellMethod(
axes=axisX,
method="mean",
qualifiers={
"interval": [cfdm.Data(1, "day")],
"comment": "ok"
},
)
cm1 = cfdm.CellMethod(axes=[axisY],
method="maximum",
qualifiers={"where": "sea"})
f.set_construct(cm0)
f.set_construct(cm1)
self.assertTrue(f.equals(f, verbose=verbose),
"Field f not equal to itself")
self.assertTrue(
f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself",
)
cfdm.write(f, self.filename, fmt="NETCDF3_CLASSIC", verbose=verbose)
g = cfdm.read(self.filename, verbose=1)
array = (g[0].constructs.filter_by_identity(
"long_name=greek_letters").value().data.array)
self.assertEqual(array[1], b"beta")
self.assertEqual(len(g), 1)
g = g[0].squeeze()
self.assertEqual(
sorted(f.constructs),
sorted(g.constructs),
"\n\nf (created in memory)\n{}\n\n{}\n\ng "
"(read from disk)\n{}\n\n{}".format(
sorted(f.constructs),
sorted(f.constructs.items()),
sorted(g.constructs),
sorted(g.constructs.items()),
),
)
self.assertTrue(
f.equals(f, verbose=verbose),
"Field f not equal to itself after having been written to disk",
)
self.assertTrue(
f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself after having been "
"written to disk",
)
self.assertTrue(
g.equals(g.copy(), verbose=verbose),
"Field g not equal to a copy of itself",
)
self.assertTrue(
g.equals(f, verbose=verbose),
"Field (f) not equal to itself read back in (g)",
)
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(
self.filename,
verbose=verbose,
extra="domain_ancillary",
warnings=warnings,
)
def test_create_field_3(self):
"""Test ab initio creation of a third variation of field."""
# Dimension coordinates
data = numpy.arange(9.0) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property("standard_name", "grid_longitude")
dim0.set_property("units", "degrees")
array = dim0.data.array
array = numpy.array([array - 0.5, array + 0.5]).transpose((1, 0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.0)))
dim1.set_property("standard_name", "grid_latitude")
dim1.set_property("units", "degrees")
dim2 = cfdm.DimensionCoordinate(
data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.0]])),
)
dim2.set_property("standard_name",
"atmosphere_hybrid_height_coordinate")
dim2.set_property("computed_standard_name", "altitude")
dim3 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.array([15.0])))
dim3.set_property("standard_name", "time")
dim3.set_property("units", "days since 2004-06-01")
dim3.set_bounds(cfdm.Bounds(data=cfdm.Data([[0, 30.0]])))
# dim3.set_geometry('climatology')
# Auxiliary coordinates
ak = cfdm.DomainAncillary(data=cfdm.Data([10.0]))
ak.set_property("units", "m")
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.0]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.0]))
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.0]])))
aux2 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(-45, 45, dtype="int32").reshape(10, 9)))
aux2.set_property("units", "degree_N")
aux2.set_property("standard_name", "latitude")
aux3 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(60, 150, dtype="int32").reshape(9, 10)))
aux3.set_property("standard_name", "longitude")
aux3.set_property("units", "degreeE")
array = numpy.ma.array(
[
"alpha",
"beta",
"gamma",
"delta",
"epsilon",
"zeta",
"eta",
"theta",
"iota",
"kappa",
],
dtype="S",
)
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property("standard_name", "greek_letters")
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1 + numpy.arange(90.0).reshape(9, 10) * 1234))
msr0.set_measure("area")
msr0.set_property("units", "km2")
# Data
data = cfdm.Data(numpy.arange(90.0).reshape(10, 9))
properties = {"units": "m s-1"}
f = cfdm.Field(properties=properties)
f.set_property("standard_name", "eastward_wind")
axisX = f.set_construct(cfdm.DomainAxis(9))
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
axisT = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=[axisX])
y = f.set_construct(dim1, axes=[axisY])
z = f.set_construct(dim2, axes=[axisZ])
f.set_construct(dim3, axes=[axisT])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=[axisZ])
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
# ref0 = cfdm.CoordinateReference(
# parameters={'grid_mapping_name': 'rotated_latitude_longitude',
# 'grid_north_pole_latitude': 38.0,
# 'grid_north_pole_longitude': 190.0,
# 'earth_radius': 6371007,},
# coordinates=[x, y, lat, lon]
# )
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
"grid_mapping_name": "rotated_latitude_longitude",
"grid_north_pole_latitude": 38.0,
"grid_north_pole_longitude": 190.0,
})
datum = cfdm.Datum(parameters={"earth_radius": 6371007})
ref0 = cfdm.CoordinateReference(
coordinate_conversion=coordinate_conversion,
datum=datum,
coordinates=[x, y, lat, lon],
)
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property("standard_name", "surface_altitude")
orog.set_property("units", "m")
orog = f.set_construct(orog, axes=[axisY, axisX])
datum1 = cfdm.Datum({"earth_radius": 6371007})
coordinate_conversion1 = cfdm.CoordinateConversion(
parameters={
"standard_name": "atmosphere_hybrid_height_coordinate",
"computed_standard_name": "altitude",
},
domain_ancillaries={
"orog": orog,
"a": ak,
"b": bk
},
)
ref1 = cfdm.CoordinateReference(
datum=datum1,
coordinate_conversion=coordinate_conversion1,
coordinates=[z],
)
ref1 = f.set_construct(ref1)
# Field ancillary variables
# g = f.transpose([1, 0])
g = f.copy()
# g.standard_name = 'ancillary0'
# g *= 0.01
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryA"
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
# g.standard_name = 'ancillary2'
# g *= 0.001
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryB"
f.set_construct(anc, axes=[axisX])
g = f[..., 0]
g = g.squeeze()
# g.standard_name = 'ancillary3'
# g *= 0.001
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryC"
f.set_construct(anc, axes=[axisY])
f.set_property("flag_values", numpy.array([1, 2, 4], "int32"))
f.set_property("flag_meanings", "a bb ccc")
f.set_property("flag_masks", [2, 1, 0])
cm0 = cfdm.CellMethod(
axes=[axisX],
method="mean",
qualifiers={
"interval": [cfdm.Data(1, "day")],
"comment": "ok"
},
)
cm1 = cfdm.CellMethod(axes=[axisY],
method="maximum",
qualifiers={"where": "sea"})
cm2 = cfdm.CellMethod(axes=[axisT],
method="maximum",
qualifiers={"within": "years"})
cm3 = cfdm.CellMethod(axes=[axisT],
method="minimum",
qualifiers={"over": "years"})
f.set_construct(cm0)
f.set_construct(cm1)
f.set_construct(cm2)
f.set_construct(cm3)
cfdm.write(f, self.filename, fmt="NETCDF3_CLASSIC", verbose=verbose)
g = cfdm.read(self.filename, verbose=verbose)
self.assertEqual(len(g), 1,
f"Read produced too many fields: {len(g)} != 1")
g = g[0].squeeze()
self.assertEqual(
sorted(f.constructs),
sorted(g.constructs),
f"\n\nf (created in memory)"
f"\n{f.constructs}"
f"\n\n{f.constructs.items()}"
f"\n\ng (read from disk)"
f"\n{g.constructs}"
f"\n\n{g.constructs.items()}",
)
self.assertTrue(
f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself",
)
self.assertTrue(
g.equals(g.copy(), verbose=verbose),
"Field g not equal to a copy of itself",
)
self.assertTrue(
g.equals(f, verbose=verbose),
"Field not equal to itself read back in",
)
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(
self.filename,
verbose=verbose,
extra=["domain_ancillary"],
warnings=warnings,
)
def test_Field__init__(self):
"""TODO DOCS."""
cfdm.Field(source="qwerty")
def test_create_field(self):
# Dimension coordinates
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.)))
dim1.set_property('standard_name', 'grid_latitude')
dim1.set_property('units', 'degrees')
data = numpy.arange(9.) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property('standard_name', 'grid_longitude')
dim0.set_property('units', 'degrees')
dim0.nc_set_variable('x')
array = dim0.data.array
array = numpy.array([array - 0.5, array + 0.5]).transpose((1, 0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim2 = cfdm.DimensionCoordinate(
data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.]])))
dim2.set_property('standard_name',
'atmosphere_hybrid_height_coordinate')
dim2.set_property('computed_standard_name', 'altitude')
# Auxiliary coordinates
ak = cfdm.DomainAncillary(data=cfdm.Data([10.]))
ak.set_property('units', 'm')
ak.id = 'atmosphere_hybrid_height_coordinate_ak'
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.]))
bk.id = 'atmosphere_hybrid_height_coordinate_bk'
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.]])))
aux2 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(-45, 45, dtype='int32').reshape(10, 9)))
aux2.set_property('units', 'degree_N')
aux2.set_property('standard_name', 'latitude')
aux3 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(
numpy.arange(60, 150, dtype='int32').reshape(9, 10)))
aux3.set_property('standard_name', 'longitude')
aux3.set_property('units', 'degreeE')
array = numpy.ma.array([
'alpha', 'beta', 'gamma', 'delta', 'epsilon', 'zeta', 'eta',
'theta', 'iota', 'kappa'
],
dtype='S')
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property('long_name', 'greek_letters')
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1 + numpy.arange(90.).reshape(9, 10) * 1234))
msr0.set_measure('area')
msr0.set_property('units', 'km2')
msr0.nc_set_variable('areacella')
# Data
data = cfdm.Data(numpy.arange(90.).reshape(10, 9))
properties = {'units': 'm s-1'}
f = cfdm.Field(properties=properties)
f.set_property('standard_name', 'eastward_wind')
da = cfdm.DomainAxis(9)
da.nc_set_dimension('grid_longitude')
axisX = f.set_construct(da)
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=axisX)
y = f.set_construct(dim1, axes=axisY)
z = f.set_construct(dim2, axes=[axisZ])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
greek = f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=axisZ)
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
'grid_mapping_name': 'rotated_latitude_longitude',
'grid_north_pole_latitude': 38.0,
'grid_north_pole_longitude': 190.0
})
datum = cfdm.Datum(parameters={'earth_radius': 6371007})
ref0 = cfdm.CoordinateReference(
coordinate_conversion=coordinate_conversion,
datum=datum,
coordinates=[x, y, lat, lon])
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property('standard_name', 'surface_altitude')
orog.set_property('units', 'm')
orog = f.set_construct(orog, axes=[axisY, axisX])
coordinate_conversion = cfdm.CoordinateConversion(parameters={
'standard_name':
'atmosphere_hybrid_height_coordinate',
'computed_standard_name':
'altitude'
},
domain_ancillaries={
'orog': orog,
'a': ak,
'b': bk
})
ref1 = cfdm.CoordinateReference(
coordinates=[z],
datum=datum,
coordinate_conversion=coordinate_conversion)
ref1 = f.set_construct(ref1)
# Field ancillary variables
g = f.copy()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property('standard_name', 'ancillaryA')
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property('long_name', 'ancillaryB')
f.set_construct(anc, axes=axisX)
g = f[..., 0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.set_property('foo', 'bar')
f.set_construct(anc, axes=[axisY])
f.set_property('flag_values', numpy.array([1, 2, 4], 'int32'))
f.set_property('flag_meanings', 'a bb ccc')
f.set_property('flag_masks', [2, 1, 0])
cm0 = cfdm.CellMethod(axes=axisX,
method='mean',
qualifiers={
'interval': [cfdm.Data(1, 'day')],
'comment': 'ok'
})
cm1 = cfdm.CellMethod(axes=[axisY],
method='maximum',
qualifiers={'where': 'sea'})
f.set_construct(cm0)
f.set_construct(cm1)
self.assertTrue(f.equals(f, verbose=verbose),
"Field f not equal to itself")
self.assertTrue(f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself")
cfdm.write(f, self.filename, fmt='NETCDF3_CLASSIC', verbose=verbose)
g = cfdm.read(self.filename, verbose=1)
array = g[0].constructs.filter_by_identity(
'long_name=greek_letters').value().data.array
self.assertEqual(array[1], b'beta',
'greek_letters = {!r}'.format(array))
self.assertEqual(
len(g), 1,
'Read produced the wrong number of fields: {} != 1'.format(len(g)))
g = g[0].squeeze()
self.assertEqual(
sorted(f.constructs), sorted(g.constructs),
'\n\nf (created in memory)\n{}\n\n{}\n\ng '
'(read from disk)\n{}\n\n{}'.format(sorted(f.constructs),
sorted(f.constructs.items()),
sorted(g.constructs),
sorted(g.constructs.items())))
self.assertTrue(
f.equals(f, verbose=verbose),
"Field f not equal to itself after having been written to disk")
self.assertTrue(
f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself after having been "
"written to disk")
self.assertTrue(g.equals(g.copy(), verbose=verbose),
"Field g not equal to a copy of itself")
self.assertTrue(g.equals(f, verbose=verbose),
"Field (f) not equal to itself read back in (g)")
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(self.filename,
verbose=verbose,
extra='domain_ancillary',
warnings=warnings)
def test_create_field_2(self):
# Dimension coordinates
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.)))
dim1.set_property('standard_name', 'projection_y_coordinate')
dim1.set_property('units', 'm')
data = numpy.arange(9.) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property('standard_name', 'projection_x_coordinate')
dim0.set_property('units', 'm')
array = dim0.data.array
array = numpy.array([array-0.5, array+0.5]).transpose((1, 0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim2 = cfdm.DimensionCoordinate(
data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.]]))
)
dim2.set_property(
'standard_name', 'atmosphere_hybrid_height_coordinate')
# Auxiliary coordinates
aux2 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(
numpy.arange(-45, 45, dtype='int32').reshape(10, 9)))
aux2.set_property('units', 'degree_N')
aux2.set_property('standard_name', 'latitude')
aux3 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(numpy.arange(
60, 150, dtype='int32').reshape(9, 10))
)
aux3.set_property('standard_name', 'longitude')
aux3.set_property('units', 'degreeE')
array = numpy.ma.array(
['alpha', 'beta', 'gamma', 'delta', 'epsilon',
'zeta', 'eta', 'theta', 'iota', 'kappa'],
dtype='S'
)
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property('standard_name', 'greek_letters')
# Domain ancillaries
ak = cfdm.DomainAncillary(data=cfdm.Data([10.]))
ak.set_property('units', 'm')
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.]))
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.]])))
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1+numpy.arange(90.).reshape(9, 10)*1234))
msr0.set_measure('area')
msr0.set_property('units', 'km2')
# Data
data = cfdm.Data(numpy.arange(90.).reshape(10, 9))
properties = {'units': 'm s-1'}
f = cfdm.Field(properties=properties)
f.set_property('standard_name', 'eastward_wind')
axisX = f.set_construct(cfdm.DomainAxis(9))
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=[axisX])
y = f.set_construct(dim1, axes=[axisY])
z = f.set_construct(dim2, axes=[axisZ])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
greek = f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=[axisZ])
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
coordinate_conversion = cfdm.CoordinateConversion(
parameters={'grid_mapping_name': "transverse_mercator",
'latitude_of_projection_origin': 49.0,
'longitude_of_central_meridian': -2.0,
'scale_factor_at_central_meridian': 0.9996012717,
'false_easting': 400000.0,
'false_northing': -100000.0,
'unit': "metre"})
datum0 = cfdm.Datum(parameters={'inverse_flattening': 299.3249646,
'longitude_of_prime_meridian': 0.0,
'semi_major_axis': 6377563.396})
ref0 = cfdm.CoordinateReference(
coordinates=[x, y],
datum=datum0,
coordinate_conversion=coordinate_conversion
)
coordinate_conversion = cfdm.CoordinateConversion(
parameters={'grid_mapping_name': "latitude_longitude"})
datum2 = cfdm.Datum(parameters={'longitude_of_prime_meridian': 0.0,
'semi_major_axis': 6378137.0,
'inverse_flattening': 298.257223563})
ref2 = cfdm.CoordinateReference(
coordinates=[lat, lon],
datum=datum2,
coordinate_conversion=coordinate_conversion)
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
f.set_construct(ref2)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property('standard_name', 'surface_altitude')
orog.set_property('units', 'm')
orog = f.set_construct(orog, axes=[axisY, axisX])
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
'standard_name': 'atmosphere_hybrid_height_coordinate'
},
domain_ancillaries={
'orog': orog,
'a': ak,
'b': bk
}
)
ref1 = cfdm.CoordinateReference(
coordinates=[z],
datum=datum0,
coordinate_conversion=coordinate_conversion
)
f.set_construct(ref1)
# Field ancillary variables
g = f.copy()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryA'
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryB'
f.set_construct(anc, axes=[axisX])
g = f[..., 0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryC'
f.set_construct(anc, axes=[axisY])
f.set_property('flag_values', numpy.array([1, 2, 4], 'int32'))
f.set_property('flag_meanings', 'a bb ccc')
f.set_property('flag_masks', [2, 1, 0])
cm0 = cfdm.CellMethod(axes=[axisX],
method='mean',
qualifiers={'interval': [cfdm.Data(1, 'day')],
'comment': 'ok'})
cm1 = cfdm.CellMethod(axes=[axisY],
method='maximum',
qualifiers={'where': 'sea'})
f.set_construct(cm0)
f.set_construct(cm1)
self.assertTrue(f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself")
for fmt in ('NETCDF3_CLASSIC',
'NETCDF3_64BIT',
'NETCDF4',
'NETCDF4_CLASSIC'):
cfdm.write(f, self.filename, fmt=fmt, verbose=verbose)
g = cfdm.read(self.filename, verbose=verbose)
self.assertEqual(len(g), 1, '{} != 1'.format(len(g)))
g = g[0].squeeze()
self.assertEqual(sorted(f.constructs), sorted(g.constructs),
'\n\nf\n{}\n\n{}\n\ng\n{}\n\n{}'.format(
sorted(f.constructs),
sorted(f.constructs.items()),
sorted(g.constructs),
sorted(g.constructs.items())))
self.assertTrue(g.equals(g.copy(), verbose=verbose),
"Field g not equal to a copy of itself")
self.assertTrue(g.equals(f, verbose=verbose),
"Field not equal to itself read back in")
# --- End: for
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(self.filename, verbose=verbose,
extra=['domain_ancillary'], warnings=warnings)
f.cell_methods()['cellmethod0'].set_property('intervals', [cfdm.Data(0.1 , 'degrees')])
f.cell_methods()['cellmethod0'].set_property('where', 'land')
f.cell_methods()['cellmethod0'].set_axes(['domainaxis1', 'domainaxis2'])
f.cell_methods()['cellmethod1'].set_property('method', 'maximum')
f.cell_methods()['cellmethod1'].del_property('where')
f.cell_methods()['cellmethod1'].set_axes([tda])
f.dump()
print(f)
h = cfdm.Field()
h.properties({'standard_name': 'specific_humidity',
'units': '1',
'project': 'research',
})
h.nc_global_attributes(['project'])
h.nc_set_variable('q')
y = h.set_domain_axis(cfdm.DomainAxis(5))
x = h.set_domain_axis(cfdm.DomainAxis(8))
t = h.set_domain_axis(cfdm.DomainAxis(1))
data = numpy.random.uniform(0, 0.15, 40).reshape(5, 8)
data[[1, 3]] /= 2.
data[[0, 4]] /= 4.
data = numpy.around(data, 3)
def test_netCDF_global_unlimited(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
# ------------------------------------------------------------
# Unlimited dimensions
# ------------------------------------------------------------
f = cfdm.Field()
self.assertTrue(f.nc_clear_unlimited_dimensions() == set())
f = cfdm.Field()
f.nc_set_unlimited_dimensions(())
f = cfdm.Field()
self.assertTrue(f.nc_unlimited_dimensions() == set())
f.nc_set_unlimited_dimensions(['qwerty', 'asdf'])
self.assertTrue(f.nc_unlimited_dimensions() == set(['qwerty', 'asdf']))
f.nc_set_unlimited_dimensions(['zxc'])
self.assertTrue(
f.nc_unlimited_dimensions() == set(['qwerty', 'asdf', 'zxc']))
self.assertTrue(f.nc_clear_unlimited_dimensions() == set(
['qwerty', 'asdf', 'zxc']))
self.assertTrue(f.nc_unlimited_dimensions() == set())
# ------------------------------------------------------------
# Global attributes
# ------------------------------------------------------------
f = cfdm.Field()
self.assertTrue(f.nc_clear_global_attributes() == {})
f.nc_set_global_attribute('Conventions')
f.nc_set_global_attribute('project', 'X')
self.assertTrue(f.nc_global_attributes() == {
'Conventions': None,
'project': 'X'
})
f.nc_set_global_attribute('project')
f.nc_set_global_attribute('comment', None)
self.assertTrue(f.nc_global_attributes() == {
'Conventions': None,
'project': None,
'comment': None
})
self.assertTrue(f.nc_clear_global_attributes() == {
'Conventions': None,
'project': None,
'comment': None
})
self.assertTrue(f.nc_global_attributes() == {})
f.nc_set_global_attribute('Conventions')
f.nc_set_global_attribute('project')
self.assertTrue(f.nc_global_attributes() == {
'Conventions': None,
'project': None
})
f = cfdm.Field()
f.set_properties({'foo': 'bar', 'comment': 'variable comment'})
f.nc_set_variable('tas')
d = f.set_construct(cfdm.DomainAxis(2))
f.set_data(cfdm.Data([8, 9]), axes=[d])
f2 = f.copy()
f2.nc_set_variable('ua')
cfdm.write([f, f2],
'tempfilename.nc',
file_descriptors={
'comment': 'global comment',
'qwerty': 'asdf'
})
g = cfdm.read('tempfilename.nc', verbose=False)
self.assertTrue(len(g) == 2)
for x in g:
self.assertTrue(
x.properties() == {
'comment': 'variable comment',
'foo': 'bar',
'qwerty': 'asdf',
'Conventions': 'CF-1.7'
})
self.assertTrue(
x.nc_global_attributes() == {
'comment': 'global comment',
'qwerty': None,
'Conventions': None
}, x.nc_global_attributes())
cfdm.write(g, 'tempfilename2.nc')
h = cfdm.read('tempfilename2.nc')
for x, y in zip(h, g):
self.assertTrue(x.properties() == y.properties())
self.assertTrue(
x.nc_global_attributes() == y.nc_global_attributes())
self.assertTrue(x.equals(y, verbose=True))
self.assertTrue(y.equals(x, verbose=True))
g[1].nc_set_global_attribute('comment', 'different comment')
cfdm.write(g, 'tempfilename3.nc')
h = cfdm.read('tempfilename3.nc')
for x, y in zip(h, g):
self.assertTrue(x.properties() == y.properties())
self.assertTrue(x.nc_global_attributes() == {
'comment': None,
'qwerty': None,
'Conventions': None
})
self.assertTrue(x.equals(y, verbose=True))
self.assertTrue(y.equals(x, verbose=True))
a
a.properties()
a.data
print("\n**Field creation**\n")
print("\n**Stage 1:** The field construct is created without metadata\n")
print("\n**Stage 2:** Metadata constructs are created independently.\n")
print("\n**Stage 3:** The metadata constructs are inserted into the field\n")
p = cfdm.Field(properties={'standard_name': 'precipitation_flux'})
p
dc = cfdm.DimensionCoordinate(properties={'long_name': 'Longitude'},
data=cfdm.Data([0, 1, 2.]))
dc
fa = cfdm.FieldAncillary(
properties={'standard_name': 'precipitation_flux status_flag'},
data=cfdm.Data(numpy.array([0, 0, 2], dtype='int8')))
fa
p = cfdm.Field()
p
p.set_property('standard_name', 'precipitation_flux')
p
dc = cfdm.DimensionCoordinate()
dc
dc.set_property('long_name', 'Longitude')
def test_create_field_2(self):
"""Test ab initio creation of a second variation of field."""
# Dimension coordinates
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.0)))
dim1.set_property("standard_name", "projection_y_coordinate")
dim1.set_property("units", "m")
data = numpy.arange(9.0) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property("standard_name", "projection_x_coordinate")
dim0.set_property("units", "m")
array = dim0.data.array
array = numpy.array([array - 0.5, array + 0.5]).transpose((1, 0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim2 = cfdm.DimensionCoordinate(
data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.0]])),
)
dim2.set_property(
"standard_name", "atmosphere_hybrid_height_coordinate"
)
# Auxiliary coordinates
aux2 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(numpy.arange(-45, 45, dtype="int32").reshape(10, 9))
)
aux2.set_property("units", "degree_N")
aux2.set_property("standard_name", "latitude")
aux3 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(numpy.arange(60, 150, dtype="int32").reshape(9, 10))
)
aux3.set_property("standard_name", "longitude")
aux3.set_property("units", "degreeE")
array = numpy.ma.array(
[
"alpha",
"beta",
"gamma",
"delta",
"epsilon",
"zeta",
"eta",
"theta",
"iota",
"kappa",
],
dtype="S",
)
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property("standard_name", "greek_letters")
# Domain ancillaries
ak = cfdm.DomainAncillary(data=cfdm.Data([10.0]))
ak.set_property("units", "m")
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.0]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.0]))
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.0]])))
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1 + numpy.arange(90.0).reshape(9, 10) * 1234)
)
msr0.set_measure("area")
msr0.set_property("units", "km2")
# Data
data = cfdm.Data(numpy.arange(90.0).reshape(10, 9))
properties = {"units": "m s-1"}
f = cfdm.Field(properties=properties)
f.set_property("standard_name", "eastward_wind")
axisX = f.set_construct(cfdm.DomainAxis(9))
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=[axisX])
y = f.set_construct(dim1, axes=[axisY])
z = f.set_construct(dim2, axes=[axisZ])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=[axisZ])
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
"grid_mapping_name": "transverse_mercator",
"latitude_of_projection_origin": 49.0,
"longitude_of_central_meridian": -2.0,
"scale_factor_at_central_meridian": 0.9996012717,
"false_easting": 400000.0,
"false_northing": -100000.0,
"unit": "metre",
}
)
datum0 = cfdm.Datum(
parameters={
"inverse_flattening": 299.3249646,
"longitude_of_prime_meridian": 0.0,
"semi_major_axis": 6377563.396,
}
)
ref0 = cfdm.CoordinateReference(
coordinates=[x, y],
datum=datum0,
coordinate_conversion=coordinate_conversion,
)
coordinate_conversion = cfdm.CoordinateConversion(
parameters={"grid_mapping_name": "latitude_longitude"}
)
datum2 = cfdm.Datum(
parameters={
"longitude_of_prime_meridian": 0.0,
"semi_major_axis": 6378137.0,
"inverse_flattening": 298.257223563,
}
)
ref2 = cfdm.CoordinateReference(
coordinates=[lat, lon],
datum=datum2,
coordinate_conversion=coordinate_conversion,
)
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
f.set_construct(ref2)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property("standard_name", "surface_altitude")
orog.set_property("units", "m")
orog = f.set_construct(orog, axes=[axisY, axisX])
coordinate_conversion = cfdm.CoordinateConversion(
parameters={
"standard_name": "atmosphere_hybrid_height_coordinate"
},
domain_ancillaries={"orog": orog, "a": ak, "b": bk},
)
ref1 = cfdm.CoordinateReference(
coordinates=[z],
datum=datum0,
coordinate_conversion=coordinate_conversion,
)
f.set_construct(ref1)
# Field ancillary variables
g = f.copy()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryA"
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryB"
f.set_construct(anc, axes=[axisX])
g = f[..., 0]
g = g.squeeze()
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = "ancillaryC"
f.set_construct(anc, axes=[axisY])
f.set_property("flag_values", numpy.array([1, 2, 4], "int32"))
f.set_property("flag_meanings", "a bb ccc")
f.set_property("flag_masks", [2, 1, 0])
cm0 = cfdm.CellMethod(
axes=[axisX],
method="mean",
qualifiers={"interval": [cfdm.Data(1, "day")], "comment": "ok"},
)
cm1 = cfdm.CellMethod(
axes=[axisY], method="maximum", qualifiers={"where": "sea"}
)
f.set_construct(cm0)
f.set_construct(cm1)
self.assertTrue(
f.equals(f.copy(), verbose=verbose),
"Field f not equal to a copy of itself",
)
for fmt in (
"NETCDF3_CLASSIC",
"NETCDF3_64BIT",
"NETCDF4",
"NETCDF4_CLASSIC",
):
cfdm.write(f, self.filename, fmt=fmt, verbose=verbose)
g = cfdm.read(self.filename, verbose=verbose)
self.assertEqual(len(g), 1, f"{len(g)} != 1")
g = g[0].squeeze()
self.assertEqual(
sorted(f.constructs),
sorted(g.constructs),
f"\n\nf (created in memory)"
f"\n{f.constructs}"
f"\n\n{f.constructs.items()}"
f"\n\ng (read from disk)"
f"\n{g.constructs}"
f"\n\n{g.constructs.items()}",
)
self.assertTrue(
g.equals(g.copy(), verbose=verbose),
"Field g not equal to a copy of itself",
)
self.assertTrue(
g.equals(f, verbose=verbose),
"Field not equal to itself read back in",
)
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(
self.filename,
verbose=verbose,
extra=["domain_ancillary"],
warnings=warnings,
)
def test_create_field_3(self):
# Dimension coordinates
data = numpy.arange(9.) + 20
data[-1] = 34
dim0 = cfdm.DimensionCoordinate(data=cfdm.Data(data))
dim0.set_property('standard_name', 'grid_longitude')
dim0.set_property('units', 'degrees')
array = dim0.data.array
array = numpy.array([array-0.5, array+0.5]).transpose((1,0))
array[-2, 1] = 30
array[-1, :] = [30, 36]
dim0.set_bounds(cfdm.Bounds(data=cfdm.Data(array)))
dim1 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.arange(10.)))
dim1.set_property('standard_name', 'grid_latitude')
dim1.set_property('units', 'degrees')
dim2 = cfdm.DimensionCoordinate(data=cfdm.Data([1.5]),
bounds=cfdm.Bounds(data=cfdm.Data([[1, 2.]])))
dim2.set_property('standard_name' , 'atmosphere_hybrid_height_coordinate')
dim2.set_property('computed_standard_name', 'altitude')
dim3 = cfdm.DimensionCoordinate(data=cfdm.Data(numpy.array([15.0])))
dim3.set_property('standard_name', 'time')
dim3.set_property('units', 'days since 2004-06-01')
dim3.set_bounds(cfdm.Bounds(data=cfdm.Data([[0, 30.]])))
# dim3.set_geometry('climatology')
# Auxiliary coordinates
ak = cfdm.DomainAncillary(data=cfdm.Data([10.]))
ak.set_property('units', 'm')
ak.set_bounds(cfdm.Bounds(data=cfdm.Data([[5, 15.]])))
bk = cfdm.DomainAncillary(data=cfdm.Data([20.]))
bk.set_bounds(cfdm.Bounds(data=cfdm.Data([[14, 26.]])))
aux2 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(numpy.arange(-45, 45, dtype='int32').reshape(10, 9)))
aux2.set_property('units', 'degree_N')
aux2.set_property('standard_name', 'latitude')
aux3 = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(numpy.arange(60, 150, dtype='int32').reshape(9, 10)))
aux3.set_property('standard_name', 'longitude')
aux3.set_property('units', 'degreeE')
array = numpy.ma.array(['alpha','beta','gamma','delta','epsilon',
'zeta','eta','theta','iota','kappa'], dtype='S')
array[0] = numpy.ma.masked
aux4 = cfdm.AuxiliaryCoordinate(data=cfdm.Data(array))
aux4.set_property('standard_name', 'greek_letters')
# Cell measures
msr0 = cfdm.CellMeasure(
data=cfdm.Data(1+numpy.arange(90.).reshape(9, 10)*1234))
msr0.set_measure('area')
msr0.set_property('units', 'km2')
# Data
data = cfdm.Data(numpy.arange(90.).reshape(10, 9))
properties = {'units': 'm s-1'}
f = cfdm.Field(properties=properties)
f.set_property('standard_name', 'eastward_wind')
axisX = f.set_construct(cfdm.DomainAxis(9))
axisY = f.set_construct(cfdm.DomainAxis(10))
axisZ = f.set_construct(cfdm.DomainAxis(1))
axisT = f.set_construct(cfdm.DomainAxis(1))
f.set_data(data, axes=[axisY, axisX])
x = f.set_construct(dim0, axes=[axisX])
y = f.set_construct(dim1, axes=[axisY])
z = f.set_construct(dim2, axes=[axisZ])
t = f.set_construct(dim3, axes=[axisT])
lat = f.set_construct(aux2, axes=[axisY, axisX])
lon = f.set_construct(aux3, axes=[axisX, axisY])
greek = f.set_construct(aux4, axes=[axisY])
ak = f.set_construct(ak, axes=[axisZ])
bk = f.set_construct(bk, axes=[axisZ])
# Coordinate references
# ref0 = cfdm.CoordinateReference(
# parameters={'grid_mapping_name': 'rotated_latitude_longitude',
# 'grid_north_pole_latitude': 38.0,
# 'grid_north_pole_longitude': 190.0,
# 'earth_radius': 6371007,},
# coordinates=[x, y, lat, lon]
# )
coordinate_conversion = cfdm.CoordinateConversion(
parameters={'grid_mapping_name': 'rotated_latitude_longitude',
'grid_north_pole_latitude': 38.0,
'grid_north_pole_longitude': 190.0})
datum = cfdm.Datum(parameters={'earth_radius': 6371007})
ref0 = cfdm.CoordinateReference(
coordinate_conversion=coordinate_conversion,
datum=datum,
coordinates=[x, y, lat, lon]
)
f.set_construct(msr0, axes=[axisX, axisY])
f.set_construct(ref0)
orog = cfdm.DomainAncillary(data=f.get_data())
orog.set_property('standard_name', 'surface_altitude')
orog.set_property('units', 'm')
orog = f.set_construct(orog, axes=[axisY, axisX])
datum1 = cfdm.Datum({'earth_radius' : 6371007})
coordinate_conversion1 = cfdm.CoordinateConversion(
parameters={'standard_name': 'atmosphere_hybrid_height_coordinate',
'computed_standard_name': 'altitude'},
domain_ancillaries={'orog': orog,
'a' : ak,
'b' : bk})
ref1 = cfdm.CoordinateReference(
datum=datum1,
coordinate_conversion=coordinate_conversion1,
coordinates=[z]
)
ref1 = f.set_construct(ref1)
# Field ancillary variables
# g = f.transpose([1, 0])
g = f.copy()
# g.standard_name = 'ancillary0'
# g *= 0.01
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryA'
f.set_construct(anc, axes=[axisY, axisX])
g = f[0]
g = g.squeeze()
# g.standard_name = 'ancillary2'
# g *= 0.001
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryB'
f.set_construct(anc, axes=[axisX])
g = f[..., 0]
g = g.squeeze()
# g.standard_name = 'ancillary3'
# g *= 0.001
anc = cfdm.FieldAncillary(data=g.get_data())
anc.standard_name = 'ancillaryC'
f.set_construct(anc, axes=[axisY])
f.set_property('flag_values', numpy.array([1, 2, 4], 'int32'))
f.set_property('flag_meanings', 'a bb ccc')
f.set_property('flag_masks', [2, 1, 0])
cm0 = cfdm.CellMethod(axes=[axisX],
method='mean',
qualifiers={'interval': [cfdm.Data(1, 'day')],
'comment' : 'ok'})
cm1 = cfdm.CellMethod(axes=[axisY],
method='maximum',
qualifiers={'where' : 'sea'})
cm2 = cfdm.CellMethod(axes=[axisT],
method='maximum',
qualifiers={'within' : 'years'})
cm3 = cfdm.CellMethod(axes=[axisT],
method='minimum',
qualifiers={'over' : 'years'})
f.set_construct(cm0)
f.set_construct(cm1)
f.set_construct(cm2)
f.set_construct(cm3)
if verbose:
print(repr(f))
print(f)
print(f.constructs)
print(f.construct_data_axes())
f.dump()
# sys.exit(0)
cfdm.write(f, self.filename, fmt='NETCDF3_CLASSIC', verbose=verbose)
g = cfdm.read(self.filename, verbose=verbose) #, squeeze=True)
if verbose:
# g[0].dump()
# sys.exit(0)
for x in g:
x.print_read_report()
self.assertTrue(len(g) == 1, 'Read produced too many fields: {} != 1'.format(len(g)))
g = g[0].squeeze()
# print g
self.assertTrue(sorted(f.constructs) == sorted(g.constructs),
'\n\nf (created in memory)\n{}\n\n{}\n\ng (read from disk)\n{}\n\n{}'.format(
sorted(f.constructs),
sorted(f.constructs.items()),
sorted(g.constructs),
sorted(g.constructs.items())))
self.assertTrue(f.equals(f.copy(), verbose=True),
"Field f not equal to a copy of itself")
self.assertTrue(g.equals(g.copy(), verbose=True),
"Field g not equal to a copy of itself")
# print f.dump()
# print'f'
# print f
# print 'g'
# print g
# f.dump()
# g.dump()
if verbose:
f.dump()
g.dump()
# sys.exit(0)
self.assertTrue(g.equals(f, verbose=True),
"Field not equal to itself read back in")
# sys.exit(0)
x = g.dump(display=False)
x = f.dump(display=False)
g = cfdm.read(self.filename, verbose=verbose,
extra=['domain_ancillary'], warnings=warnings)
if verbose:
for x in g:
x.print_read_report()
print(g)
g[0].dump()
def test_Field__init__(self):
"""Test the Field constructor and source keyword."""
cfdm.Field(source="qwerty")
def test_netCDF_variable_dimension(self):
"""Test variable and dimension access NetCDF methods."""
f = cfdm.Field()
f.nc_set_variable("qwerty")
self.assertTrue(f.nc_has_variable())
self.assertEqual(f.nc_get_variable(), "qwerty")
self.assertEqual(f.nc_get_variable(default=None), "qwerty")
self.assertEqual(f.nc_del_variable(), "qwerty")
self.assertFalse(f.nc_has_variable())
self.assertIsNone(f.nc_get_variable(default=None))
self.assertIsNone(f.nc_del_variable(default=None))
f.nc_set_variable("/ncvar")
self.assertEqual(f.nc_get_variable(), "ncvar")
f.nc_set_variable("/ncvar/qwerty")
self.assertEqual(f.nc_get_variable(), "/ncvar/qwerty")
for nc_var_name in self.nc_grouped_variable_names:
with self.assertRaises(ValueError):
f.nc_set_variable(nc_var_name)
d = cfdm.DomainAxis()
d.nc_set_dimension("qwerty")
self.assertTrue(d.nc_has_dimension())
self.assertEqual(d.nc_get_dimension(), "qwerty")
self.assertEqual(d.nc_get_dimension(default=None), "qwerty")
self.assertEqual(d.nc_del_dimension(), "qwerty")
self.assertFalse(d.nc_has_dimension())
self.assertIsNone(d.nc_get_dimension(default=None))
self.assertIsNone(d.nc_del_dimension(default=None))
d.nc_set_dimension("/ncdim")
self.assertEqual(d.nc_get_dimension(), "ncdim")
d.nc_set_dimension("/ncdim/qwerty")
self.assertEqual(d.nc_get_dimension(), "/ncdim/qwerty")
for nc_dim_name in self.nc_grouped_dimension_names:
with self.assertRaises(ValueError):
d.nc_set_dimension(nc_dim_name)
d = cfdm.Count()
d.nc_set_sample_dimension("qwerty")
self.assertTrue(d.nc_has_sample_dimension())
self.assertEqual(d.nc_get_sample_dimension(), "qwerty")
self.assertEqual(d.nc_get_sample_dimension(default=None), "qwerty")
self.assertEqual(d.nc_del_sample_dimension(), "qwerty")
self.assertFalse(d.nc_has_sample_dimension())
self.assertIsNone(d.nc_get_sample_dimension(default=None))
self.assertIsNone(d.nc_del_sample_dimension(default=None))
d.nc_set_sample_dimension("/ncdim")
self.assertEqual(d.nc_get_sample_dimension(), "ncdim")
d.nc_set_sample_dimension("/ncdim/qwerty")
self.assertEqual(d.nc_get_sample_dimension(), "/ncdim/qwerty")
for nc_dim_name in self.nc_grouped_dimension_names:
with self.assertRaises(ValueError):
d.nc_set_sample_dimension(nc_dim_name)
# ------------------------------------------------------------
# Global attributes
# ------------------------------------------------------------
# values keyword
f = cfdm.Field()
f.nc_set_global_attribute("Conventions", "CF-1.8")
f.nc_set_global_attribute("project")
f.nc_set_global_attribute("foo")
f.set_property("Conventions", "Y")
f.set_property("project", "X")
self.assertEqual(
f.nc_global_attributes(values=True),
{"Conventions": "CF-1.8", "project": "X", "foo": None},
)
f = cfdm.Field()
self.assertEqual(f.nc_clear_global_attributes(), {})
f.nc_set_global_attribute("Conventions")
f.nc_set_global_attribute("project", "X")
self.assertEqual(
f.nc_global_attributes(), {"Conventions": None, "project": "X"}
)
f.nc_set_global_attribute("project")
f.nc_set_global_attribute("comment", None)
self.assertEqual(
f.nc_global_attributes(),
{"Conventions": None, "project": None, "comment": None},
)
self.assertEqual(
f.nc_clear_global_attributes(),
{"Conventions": None, "project": None, "comment": None},
)
self.assertEqual(f.nc_global_attributes(), {})
f.nc_set_global_attribute("Conventions")
f.nc_set_global_attribute("project")
self.assertEqual(
f.nc_global_attributes(), {"Conventions": None, "project": None}
)
_ = f.nc_clear_global_attributes()
f.nc_set_global_attributes({})
self.assertEqual(f.nc_global_attributes(), {})
f.nc_set_global_attributes({"comment": 123}, copy=False)
self.assertEqual(f.nc_global_attributes(), {"comment": 123})
f.nc_set_global_attributes({"comment": None, "foo": "bar"})
self.assertEqual(
f.nc_global_attributes(), {"comment": None, "foo": "bar"}
)
f = cfdm.Field()
f.set_properties({"foo": "bar", "comment": "variable comment"})
f.nc_set_variable("tas")
d = f.set_construct(cfdm.DomainAxis(2))
f.set_data(cfdm.Data([8, 9]), axes=[d])
f2 = f.copy()
f2.nc_set_variable("ua")
cfdm.write(
[f, f2],
tempfile1,
file_descriptors={"comment": "global comment", "qwerty": "asdf"},
)
g = cfdm.read(tempfile1)
self.assertEqual(len(g), 2)
for x in g:
self.assertEqual(
x.properties(),
{
"comment": "variable comment",
"foo": "bar",
"qwerty": "asdf",
"Conventions": "CF-" + cfdm.CF(),
},
)
self.assertEqual(
x.nc_global_attributes(),
{
"comment": "global comment",
"qwerty": None,
"Conventions": None,
},
)
cfdm.write(g, tempfile2)
h = cfdm.read(tempfile2)
for x, y in zip(h, g):
self.assertEqual(x.properties(), y.properties())
self.assertEqual(
x.nc_global_attributes(), y.nc_global_attributes()
)
self.assertTrue(x.equals(y, verbose=3))
self.assertTrue(y.equals(x, verbose=3))
g[1].nc_set_global_attribute("comment", "different comment")
cfdm.write(g, tempfile3)
h = cfdm.read(tempfile3)
for x, y in zip(h, g):
self.assertEqual(x.properties(), y.properties())
self.assertEqual(
x.nc_global_attributes(),
{"comment": None, "qwerty": None, "Conventions": None},
)
self.assertTrue(x.equals(y, verbose=3))
self.assertTrue(y.equals(x, verbose=3))
def test_Field__init__(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
f = cfdm.Field(source='qwerty')