def test_DSG_create_contiguous(self):
"""Test the creation of a contiguous ragged array."""
# Define the ragged array values
ragged_array = numpy.array([1, 3, 4, 3, 6], dtype="float32")
# Define the count array values
count_array = [2, 3]
# Initialise the count variable
count_variable = cfdm.Count(data=cfdm.Data(count_array))
count_variable.set_property(
"long_name", "number of obs for this timeseries"
)
# Initialise the contiguous ragged array object
array = cfdm.RaggedContiguousArray(
compressed_array=cfdm.Data(ragged_array),
shape=(2, 3),
size=6,
ndim=2,
count_variable=count_variable,
)
# Initialize the auxiliary coordinate construct with the
# ragged array and set some properties
z = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(array),
properties={
"standard_name": "height",
"units": "km",
"positive": "up",
},
)
self.assertTrue(
(
z.data.array
== numpy.ma.masked_array(
data=[[1.0, 3.0, 99], [4.0, 3.0, 6.0]],
mask=[[False, False, True], [False, False, False]],
fill_value=1e20,
dtype="float32",
)
).all()
)
self.assertEqual(z.data.get_compression_type(), "ragged contiguous")
self.assertTrue(
(
z.data.compressed_array
== numpy.array([1.0, 3.0, 4.0, 3.0, 6.0], dtype="float32")
).all()
)
self.assertTrue(
(z.data.get_count().data.array == numpy.array([2, 3])).all()
)
def test_AuxiliaryCoordinate_interior_ring(self):
c = cfdm.AuxiliaryCoordinate()
i = cfdm.InteriorRing(data=cfdm.Data(numpy.arange(10).reshape(5, 2)))
c.set_interior_ring(i)
self.assertTrue(c.has_interior_ring())
self.assertIsInstance(c.get_interior_ring(), cfdm.InteriorRing)
self.assertIsInstance(c.del_interior_ring(None), cfdm.InteriorRing)
self.assertFalse(c.has_interior_ring())
self.assertIsNone(c.del_interior_ring(None))
def test_AuxiliaryCoordinate_insert_dimension(self):
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates('grid_longitude').value()
x = cfdm.AuxiliaryCoordinate(source=d)
self.assertEqual(x.shape, (9,))
self.assertEqual(x.bounds.shape, (9, 2))
y = x.insert_dimension(0)
self.assertEqual(y.shape, (1, 9))
self.assertEqual(y.bounds.shape, (1, 9, 2), y.bounds.shape)
x.insert_dimension(-1, inplace=True)
self.assertEqual(x.shape, (9, 1))
self.assertEqual(x.bounds.shape, (9, 1, 2), x.bounds.shape)
def test_DSG_create_contiguous(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
# Define the ragged array values
ragged_array = numpy.array([1, 3, 4, 3, 6], dtype='float32')
# Define the count array values
count_array = [2, 3]
# Initialise the count variable
count_variable = cfdm.Count(data=cfdm.Data(count_array))
count_variable.set_property('long_name',
'number of obs for this timeseries')
# Initialise the contiguous ragged array object
array = cfdm.RaggedContiguousArray(
compressed_array=cfdm.Data(ragged_array),
shape=(2, 3), size=6, ndim=2,
count_variable=count_variable)
# Initialize the auxiliary coordinate construct with the
# ragged array and set some properties
z = cfdm.AuxiliaryCoordinate(
data=cfdm.Data(array),
properties={'standard_name': 'height',
'units': 'km',
'positive': 'up'})
self.assertTrue((z.data.array == numpy.ma.masked_array(
data=[[1.0, 3.0, 99],
[4.0, 3.0, 6.0]],
mask=[[False, False, True],
[False, False, False]],
fill_value=1e+20,
dtype='float32')).all())
self.assertEqual(z.data.get_compression_type(), 'ragged contiguous')
self.assertTrue((z.data.compressed_array == numpy.array(
[1., 3., 4., 3., 6.], dtype='float32')).all())
self.assertTrue((z.data.get_count().data.array == numpy.array(
[2, 3])).all())
"units": "degrees"
},
data=cfdm.Data(numpy.arange(9.0)),
bounds=cfdm.Bounds(data=cfdm.Data(numpy.arange(18).reshape(9, 2))),
)
dim_T = tas.set_construct(dimension_coordinate_T, axes=axis_T)
dim_Z = tas.set_construct(dimension_coordinate_Z, axes=axis_Z)
dim_Y = tas.set_construct(dimension_coordinate_Y, axes=axis_Y)
dim_X = tas.set_construct(dimension_coordinate_X, axes=axis_X)
# Create and set the auxiliary coordinate constructs
auxiliary_coordinate_lat = cfdm.AuxiliaryCoordinate(
properties={
"standard_name": "latitude",
"units": "degrees_north"
},
data=cfdm.Data(numpy.arange(90.0).reshape(10, 9)),
)
auxiliary_coordinate_lon = cfdm.AuxiliaryCoordinate(
properties={
"standard_name": "longitude",
"units": "degrees_east"
},
data=cfdm.Data(numpy.arange(90.0).reshape(9, 10)),
)
array = numpy.ma.array(list("abcdefghij"))
array[0] = numpy.ma.masked
auxiliary_coordinate_name = cfdm.AuxiliaryCoordinate(
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):
"""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_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(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_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()
class AuxiliaryCoordinateTest(unittest.TestCase):
filename = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'test_file.nc')
aux1 = cfdm.AuxiliaryCoordinate()
aux1.standard_name = 'latitude'
a = numpy.array(
[-30, -23.5, -17.8123, -11.3345, -0.7, -0.2, 0, 0.2, 0.7,
11.30003, 17.8678678, 23.5, 30]
)
aux1.set_data(cfdm.Data(a, 'degrees_north'))
bounds = cfdm.Bounds()
b = numpy.empty(a.shape + (2,))
b[:, 0] = a - 0.1
b[:, 1] = a + 0.1
bounds.set_data(cfdm.Data(b))
aux1.set_bounds(bounds)
def setUp(self):
# Disable log messages to silence expected warnings
cfdm.log_level('DISABLE')
# Note: to enable all messages for given methods, lines or
# calls (those without a 'verbose' option to do the same)
# e.g. to debug them, wrap them (for methods, start-to-end
# internally) as follows:
#
# cfdm.LOG_LEVEL('DEBUG')
# < ... test code ... >
# cfdm.log_level('DISABLE')
def test_AuxiliaryCoordinate__repr__str__dump(self):
f = cfdm.read(self.filename, verbose=1)[0]
x = f.auxiliary_coordinates('latitude').value()
_ = repr(x)
_ = str(x)
self.assertIsInstance(x.dump(display=False), str)
self.assertIsInstance(x.dump(display=False, _title=None), str)
def test_AuxiliaryCoordinate_bounds(self):
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates('grid_longitude').value()
x = cfdm.AuxiliaryCoordinate(source=d)
def test_AuxiliaryCoordinate_properties(self):
f = cfdm.read(self.filename)[0]
x = f.auxiliary_coordinates('latitude').value()
x.set_property('long_name', 'qwerty')
self.assertEqual(x.get_property('long_name'), 'qwerty')
self.assertEqual(x.del_property('long_name'), 'qwerty')
self.assertIsNone(x.get_property('long_name', None))
self.assertIsNone(x.del_property('long_name', None))
def test_AuxiliaryCoordinate_source(self):
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates('grid_longitude').value()
x = cfdm.AuxiliaryCoordinate(source=d)
def test_AuxiliaryCoordinate_insert_dimension(self):
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates('grid_longitude').value()
x = cfdm.AuxiliaryCoordinate(source=d)
self.assertEqual(x.shape, (9,))
self.assertEqual(x.bounds.shape, (9, 2))
y = x.insert_dimension(0)
self.assertEqual(y.shape, (1, 9))
self.assertEqual(y.bounds.shape, (1, 9, 2), y.bounds.shape)
x.insert_dimension(-1, inplace=True)
self.assertEqual(x.shape, (9, 1))
self.assertEqual(x.bounds.shape, (9, 1, 2), x.bounds.shape)
def test_AuxiliaryCoordinate_transpose(self):
f = cfdm.read(self.filename)[0]
x = f.auxiliary_coordinates('longitude').value()
bounds = cfdm.Bounds(
data=cfdm.Data(numpy.arange(9*10*4).reshape(9, 10, 4)))
x.set_bounds(bounds)
self.assertEqual(x.shape, (9, 10))
self.assertEqual(x.bounds.shape, (9, 10, 4))
y = x.transpose()
self.assertEqual(y.shape, (10, 9))
self.assertEqual(y.bounds.shape, (10, 9, 4), y.bounds.shape)
x.transpose([1, 0], inplace=True)
self.assertEqual(x.shape, (10, 9))
self.assertEqual(x.bounds.shape, (10, 9, 4), x.bounds.shape)
def test_AuxiliaryCoordinate_squeeze(self):
f = cfdm.read(self.filename)[0]
x = f.auxiliary_coordinates('longitude').value()
bounds = cfdm.Bounds(
data=cfdm.Data(numpy.arange(9*10*4).reshape(9, 10, 4)))
x.set_bounds(bounds)
x.insert_dimension(1, inplace=True)
x.insert_dimension(0, inplace=True)
self.assertEqual(x.shape, (1, 9, 1, 10))
self.assertEqual(x.bounds.shape, (1, 9, 1, 10, 4))
y = x.squeeze()
self.assertEqual(y.shape, (9, 10))
self.assertEqual(y.bounds.shape, (9, 10, 4), y.bounds.shape)
x.squeeze(2, inplace=True)
self.assertEqual(x.shape, (1, 9, 10))
self.assertEqual(x.bounds.shape, (1, 9, 10, 4), x.bounds.shape)
def test_AuxiliaryCoordinate_interior_ring(self):
c = cfdm.AuxiliaryCoordinate()
i = cfdm.InteriorRing(data=cfdm.Data(numpy.arange(10).reshape(5, 2)))
c.set_interior_ring(i)
self.assertTrue(c.has_interior_ring())
self.assertIsInstance(c.get_interior_ring(), cfdm.InteriorRing)
self.assertIsInstance(c.del_interior_ring(None), cfdm.InteriorRing)
self.assertFalse(c.has_interior_ring())
self.assertIsNone(c.del_interior_ring(None))
def test_AuxiliaryCoordinate_source(self):
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates('grid_longitude').value()
x = cfdm.AuxiliaryCoordinate(source=d)
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)
def test_AuxiliaryCoordinate_source(self):
"""Test the source keyword argument to AuxiliaryCoordinate."""
f = cfdm.read(self.filename)[0]
d = f.dimension_coordinates("grid_longitude").value()
cfdm.AuxiliaryCoordinate(source=d)
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)
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.)),
bounds=cfdm.Bounds(data=cfdm.Data(numpy.arange(18).reshape(9, 2))))
dim_T = tas.set_construct(dimension_coordinate_T, axes=axis_T)
dim_Z = tas.set_construct(dimension_coordinate_Z, axes=axis_Z)
dim_Y = tas.set_construct(dimension_coordinate_Y, axes=axis_Y)
dim_X = tas.set_construct(dimension_coordinate_X, axes=axis_X)
# Create and set the auxiliary coordinate constructs
auxiliary_coordinate_lat = cfdm.AuxiliaryCoordinate(
properties={'standard_name': 'latitude',
'units': 'degrees_north'},
data=cfdm.Data(numpy.arange(90.).reshape(10, 9)))
auxiliary_coordinate_lon = cfdm.AuxiliaryCoordinate(
properties={'standard_name': 'longitude',
'units': 'degrees_east'},
data=cfdm.Data(numpy.arange(90.).reshape(9, 10)))
array = numpy.ma.array(list('abcdefghij'))
array[0] = numpy.ma.masked
auxiliary_coordinate_name = cfdm.AuxiliaryCoordinate(
properties={'long_name': 'Grid latitude name'},
data=cfdm.Data(array))
aux_LAT = tas.set_construct(auxiliary_coordinate_lat, axes=[axis_Y, axis_X])
aux_LON = tas.set_construct(auxiliary_coordinate_lon, axes=[axis_X, axis_Y])
def test_STRING(self):
if self.test_only and inspect.stack()[0][3] not in self.test_only:
return
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
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 data
tas.set_data(cfdm.Data(numpy.arange(90.).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.)),
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.)),
bounds=cfdm.Bounds(
data=cfdm.Data(numpy.arange(18).reshape(9, 2))))
dim_Y = tas.set_construct(dimension_coordinate_Y, axes=[axis_Y])
dim_X = 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)
