# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Module to support the loading of a NetCDF file into an Iris cube.
See also: `netCDF4 python <https://github.com/Unidata/netcdf4-python>`_
Also refer to document 'NetCDF Climate and Forecast (CF) Metadata Conventions'.
"""
import collections
from itertools import repeat, zip_longest
import os
import os.path
import re
import string
import warnings
import cf_units
import dask.array as da
import netCDF4
import numpy as np
import numpy.ma as ma
from iris._lazy_data import as_lazy_data
from iris.aux_factory import (
AtmosphereSigmaFactory,
HybridHeightFactory,
HybridPressureFactory,
OceanSFactory,
OceanSg1Factory,
OceanSg2Factory,
OceanSigmaFactory,
OceanSigmaZFactory,
)
import iris.config
import iris.coord_systems
import iris.coords
import iris.exceptions
import iris.fileformats.cf
import iris.io
import iris.util
# Show actions activation statistics.
DEBUG = False
# Standard CML spatio-temporal axis names.
SPATIO_TEMPORAL_AXES = ["t", "z", "y", "x"]
# Pass through CF attributes:
# - comment
# - Conventions
# - flag_masks
# - flag_meanings
# - flag_values
# - history
# - institution
# - reference
# - source
# - title
# - positive
#
_CF_ATTRS = [
"add_offset",
"ancillary_variables",
"axis",
"bounds",
"calendar",
"cell_measures",
"cell_methods",
"climatology",
"compress",
"coordinates",
"_FillValue",
"formula_terms",
"grid_mapping",
"leap_month",
"leap_year",
"long_name",
"missing_value",
"month_lengths",
"scale_factor",
"standard_error_multiplier",
"standard_name",
"units",
]
# CF attributes that should not be global.
_CF_DATA_ATTRS = [
"flag_masks",
"flag_meanings",
"flag_values",
"instance_dimension",
"missing_value",
"sample_dimension",
"standard_error_multiplier",
]
# CF attributes that should only be global.
_CF_GLOBAL_ATTRS = ["conventions", "featureType", "history", "title"]
# UKMO specific attributes that should not be global.
_UKMO_DATA_ATTRS = ["STASH", "um_stash_source", "ukmo__process_flags"]
CF_CONVENTIONS_VERSION = "CF-1.7"
_FactoryDefn = collections.namedtuple(
"_FactoryDefn", ("primary", "std_name", "formula_terms_format")
)
_FACTORY_DEFNS = {
AtmosphereSigmaFactory: _FactoryDefn(
primary="sigma",
std_name="atmosphere_sigma_coordinate",
formula_terms_format="ptop: {pressure_at_top} sigma: {sigma} "
"ps: {surface_air_pressure}",
),
HybridHeightFactory: _FactoryDefn(
primary="delta",
std_name="atmosphere_hybrid_height_coordinate",
formula_terms_format="a: {delta} b: {sigma} orog: {orography}",
),
HybridPressureFactory: _FactoryDefn(
primary="delta",
std_name="atmosphere_hybrid_sigma_pressure_coordinate",
formula_terms_format="ap: {delta} b: {sigma} "
"ps: {surface_air_pressure}",
),
OceanSigmaZFactory: _FactoryDefn(
primary="zlev",
std_name="ocean_sigma_z_coordinate",
formula_terms_format="sigma: {sigma} eta: {eta} depth: {depth} "
"depth_c: {depth_c} nsigma: {nsigma} zlev: {zlev}",
),
OceanSigmaFactory: _FactoryDefn(
primary="sigma",
std_name="ocean_sigma_coordinate",
formula_terms_format="sigma: {sigma} eta: {eta} depth: {depth}",
),
OceanSFactory: _FactoryDefn(
primary="s",
std_name="ocean_s_coordinate",
formula_terms_format="s: {s} eta: {eta} depth: {depth} a: {a} b: {b} "
"depth_c: {depth_c}",
),
OceanSg1Factory: _FactoryDefn(
primary="s",
std_name="ocean_s_coordinate_g1",
formula_terms_format="s: {s} c: {c} eta: {eta} depth: {depth} "
"depth_c: {depth_c}",
),
OceanSg2Factory: _FactoryDefn(
primary="s",
std_name="ocean_s_coordinate_g2",
formula_terms_format="s: {s} c: {c} eta: {eta} depth: {depth} "
"depth_c: {depth_c}",
),
}
# Cell methods.
_CM_KNOWN_METHODS = [
"point",
"sum",
"mean",
"maximum",
"minimum",
"mid_range",
"standard_deviation",
"variance",
"mode",
"median",
]
_CM_COMMENT = "comment"
_CM_EXTRA = "extra"
_CM_INTERVAL = "interval"
_CM_METHOD = "method"
_CM_NAME = "name"
_CM_PARSE = re.compile(
r"""
(?P<name>([\w_]+\s*?:\s+)+)
(?P<method>[\w_\s]+(?![\w_]*\s*?:))\s*
(?:
\(\s*
(?P<extra>[^\)]+)
\)\s*
)?
""",
re.VERBOSE,
)
[docs]class UnknownCellMethodWarning(Warning):
pass
[docs]def parse_cell_methods(nc_cell_methods):
"""
Parse a CF cell_methods attribute string into a tuple of zero or
more CellMethod instances.
Args:
* nc_cell_methods (str):
The value of the cell methods attribute to be parsed.
Returns:
* cell_methods
An iterable of :class:`iris.coords.CellMethod`.
Multiple coordinates, intervals and comments are supported.
If a method has a non-standard name a warning will be issued, but the
results are not affected.
"""
cell_methods = []
if nc_cell_methods is not None:
for m in _CM_PARSE.finditer(nc_cell_methods):
d = m.groupdict()
method = d[_CM_METHOD]
method = method.strip()
# Check validity of method, allowing for multi-part methods
# e.g. mean over years.
method_words = method.split()
if method_words[0].lower() not in _CM_KNOWN_METHODS:
msg = "NetCDF variable contains unknown cell method {!r}"
warnings.warn(
msg.format("{}".format(method_words[0])),
UnknownCellMethodWarning,
)
d[_CM_METHOD] = method
name = d[_CM_NAME]
name = name.replace(" ", "")
name = name.rstrip(":")
d[_CM_NAME] = tuple([n for n in name.split(":")])
interval = []
comment = []
if d[_CM_EXTRA] is not None:
#
# tokenise the key words and field colon marker
#
d[_CM_EXTRA] = d[_CM_EXTRA].replace(
"comment:", "<<comment>><<:>>"
)
d[_CM_EXTRA] = d[_CM_EXTRA].replace(
"interval:", "<<interval>><<:>>"
)
d[_CM_EXTRA] = d[_CM_EXTRA].split("<<:>>")
if len(d[_CM_EXTRA]) == 1:
comment.extend(d[_CM_EXTRA])
else:
next_field_type = comment
for field in d[_CM_EXTRA]:
field_type = next_field_type
index = field.rfind("<<interval>>")
if index == 0:
next_field_type = interval
continue
elif index > 0:
next_field_type = interval
else:
index = field.rfind("<<comment>>")
if index == 0:
next_field_type = comment
continue
elif index > 0:
next_field_type = comment
if index != -1:
field = field[:index]
field_type.append(field.strip())
#
# cater for a shared interval over multiple axes
#
if len(interval):
if len(d[_CM_NAME]) != len(interval) and len(interval) == 1:
interval = interval * len(d[_CM_NAME])
#
# cater for a shared comment over multiple axes
#
if len(comment):
if len(d[_CM_NAME]) != len(comment) and len(comment) == 1:
comment = comment * len(d[_CM_NAME])
d[_CM_INTERVAL] = tuple(interval)
d[_CM_COMMENT] = tuple(comment)
cell_method = iris.coords.CellMethod(
d[_CM_METHOD],
coords=d[_CM_NAME],
intervals=d[_CM_INTERVAL],
comments=d[_CM_COMMENT],
)
cell_methods.append(cell_method)
return tuple(cell_methods)
[docs]class CFNameCoordMap:
"""Provide a simple CF name to CF coordinate mapping."""
_Map = collections.namedtuple("_Map", ["name", "coord"])
def __init__(self):
self._map = []
[docs] def append(self, name, coord):
"""
Append the given name and coordinate pair to the mapping.
Args:
* name:
CF name of the associated coordinate.
* coord:
The coordinate of the associated CF name.
Returns:
None.
"""
self._map.append(CFNameCoordMap._Map(name, coord))
@property
def names(self):
"""Return all the CF names."""
return [pair.name for pair in self._map]
@property
def coords(self):
"""Return all the coordinates."""
return [pair.coord for pair in self._map]
[docs] def name(self, coord):
"""
Return the CF name, given a coordinate
Args:
* coord:
The coordinate of the associated CF name.
Returns:
Coordinate.
"""
result = None
for pair in self._map:
if coord == pair.coord:
result = pair.name
break
if result is None:
msg = "Coordinate is not mapped, {!r}".format(coord)
raise KeyError(msg)
return result
[docs] def coord(self, name):
"""
Return the coordinate, given a CF name.
Args:
* name:
CF name of the associated coordinate.
Returns:
CF name.
"""
result = None
for pair in self._map:
if name == pair.name:
result = pair.coord
break
if result is None:
msg = "Name is not mapped, {!r}".format(name)
raise KeyError(msg)
return result
def _actions_engine():
# Return an 'actions engine', which provides a pyke-rules-like interface to
# the core cf translation code.
# Deferred import to avoid circularity.
import iris.fileformats._nc_load_rules.engine as nc_actions_engine
engine = nc_actions_engine.Engine()
return engine
[docs]class NetCDFDataProxy:
"""A reference to the data payload of a single NetCDF file variable."""
__slots__ = ("shape", "dtype", "path", "variable_name", "fill_value")
def __init__(self, shape, dtype, path, variable_name, fill_value):
self.shape = shape
self.dtype = dtype
self.path = path
self.variable_name = variable_name
self.fill_value = fill_value
@property
def ndim(self):
return len(self.shape)
def __getitem__(self, keys):
dataset = netCDF4.Dataset(self.path)
try:
variable = dataset.variables[self.variable_name]
# Get the NetCDF variable data and slice.
var = variable[keys]
finally:
dataset.close()
return np.asanyarray(var)
def __repr__(self):
fmt = (
"<{self.__class__.__name__} shape={self.shape}"
" dtype={self.dtype!r} path={self.path!r}"
" variable_name={self.variable_name!r}>"
)
return fmt.format(self=self)
def __getstate__(self):
return {attr: getattr(self, attr) for attr in self.__slots__}
def __setstate__(self, state):
for key, value in state.items():
setattr(self, key, value)
def _assert_case_specific_facts(engine, cf, cf_group):
# Initialise a data store for built cube elements.
# This is used to patch element attributes *not* setup by the actions
# process, after the actions code has run.
engine.cube_parts["coordinates"] = []
engine.cube_parts["cell_measures"] = []
engine.cube_parts["ancillary_variables"] = []
# Assert facts for CF coordinates.
for cf_name in cf_group.coordinates.keys():
engine.add_case_specific_fact("coordinate", (cf_name,))
# Assert facts for CF auxiliary coordinates.
for cf_name in cf_group.auxiliary_coordinates.keys():
engine.add_case_specific_fact("auxiliary_coordinate", (cf_name,))
# Assert facts for CF cell measures.
for cf_name in cf_group.cell_measures.keys():
engine.add_case_specific_fact("cell_measure", (cf_name,))
# Assert facts for CF ancillary variables.
for cf_name in cf_group.ancillary_variables.keys():
engine.add_case_specific_fact("ancillary_variable", (cf_name,))
# Assert facts for CF grid_mappings.
for cf_name in cf_group.grid_mappings.keys():
engine.add_case_specific_fact("grid_mapping", (cf_name,))
# Assert facts for CF labels.
for cf_name in cf_group.labels.keys():
engine.add_case_specific_fact("label", (cf_name,))
# Assert facts for CF formula terms associated with the cf_group
# of the CF data variable.
# Collect varnames of formula-root variables as we go.
# NOTE: use dictionary keys as an 'OrderedSet'
# - see: https://stackoverflow.com/a/53657523/2615050
# This is to ensure that we can handle the resulting facts in a definite
# order, as using a 'set' led to indeterminate results.
formula_root = {}
for cf_var in cf.cf_group.formula_terms.values():
for cf_root, cf_term in cf_var.cf_terms_by_root.items():
# Only assert this fact if the formula root variable is
# defined in the CF group of the CF data variable.
if cf_root in cf_group:
formula_root[cf_root] = True
engine.add_case_specific_fact(
"formula_term",
(cf_var.cf_name, cf_root, cf_term),
)
for cf_root in formula_root.keys():
engine.add_case_specific_fact("formula_root", (cf_root,))
def _actions_activation_stats(engine, cf_name):
print("-" * 80)
print("CF Data Variable: %r" % cf_name)
engine.print_stats()
print("Rules Triggered:")
for rule in sorted(list(engine.rule_triggered)):
print("\t%s" % rule)
print("Case Specific Facts:")
kb_facts = engine.get_kb()
for key in kb_facts.entity_lists.keys():
for arg in kb_facts.entity_lists[key].case_specific_facts:
print("\t%s%s" % (key, arg))
def _set_attributes(attributes, key, value):
"""Set attributes dictionary, converting unicode strings appropriately."""
if isinstance(value, str):
try:
attributes[str(key)] = str(value)
except UnicodeEncodeError:
attributes[str(key)] = value
else:
attributes[str(key)] = value
def _get_actual_dtype(cf_var):
# Figure out what the eventual data type will be after any scale/offset
# transforms.
dummy_data = np.zeros(1, dtype=cf_var.dtype)
if hasattr(cf_var, "scale_factor"):
dummy_data = cf_var.scale_factor * dummy_data
if hasattr(cf_var, "add_offset"):
dummy_data = cf_var.add_offset + dummy_data
return dummy_data.dtype
def _get_cf_var_data(cf_var, filename):
# Get lazy chunked data out of a cf variable.
dtype = _get_actual_dtype(cf_var)
# Create cube with deferred data, but no metadata
fill_value = getattr(
cf_var.cf_data,
"_FillValue",
netCDF4.default_fillvals[cf_var.dtype.str[1:]],
)
proxy = NetCDFDataProxy(
cf_var.shape, dtype, filename, cf_var.cf_name, fill_value
)
# Get the chunking specified for the variable : this is either a shape, or
# maybe the string "contiguous".
chunks = cf_var.cf_data.chunking()
# In the "contiguous" case, pass chunks=None to 'as_lazy_data'.
if chunks == "contiguous":
chunks = None
return as_lazy_data(proxy, chunks=chunks)
[docs]class OrderedAddableList(list):
# Used purely in actions debugging, to accumulate a record of which actions
# were activated.
# It replaces a set, so as to record the ordering of operations, with
# possible repeats, and it also numbers the entries.
# Actions routines invoke the 'add' method, which thus effectively converts
# a set.add into a list.append.
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._n_add = 0
[docs] def add(self, msg):
self._n_add += 1
n_add = self._n_add
self.append(f"#{n_add:03d} : {msg}")
def _load_cube(engine, cf, cf_var, filename):
from iris.cube import Cube
"""Create the cube associated with the CF-netCDF data variable."""
data = _get_cf_var_data(cf_var, filename)
cube = Cube(data)
# Reset the actions engine.
engine.reset()
# Initialise engine rule processing hooks.
engine.cf_var = cf_var
engine.cube = cube
engine.cube_parts = {}
engine.requires = {}
engine.rule_triggered = OrderedAddableList()
engine.filename = filename
# Assert all the case-specific facts.
# This extracts 'facts' specific to this data-variable (aka cube), from
# the info supplied in the CFGroup object.
_assert_case_specific_facts(engine, cf, cf_var.cf_group)
# Run the actions engine.
# This creates various cube elements and attaches them to the cube.
# It also records various other info on the engine, to be processed later.
engine.activate()
# Having run the rules, now populate the attributes of all the cf elements with the
# "unused" attributes from the associated CF-netCDF variable.
# That is, all those that aren't CF reserved terms.
def attribute_predicate(item):
return item[0] not in _CF_ATTRS
def add_unused_attributes(iris_object, cf_var):
tmpvar = filter(attribute_predicate, cf_var.cf_attrs_unused())
for attr_name, attr_value in tmpvar:
_set_attributes(iris_object.attributes, attr_name, attr_value)
def fix_attributes_all_elements(role_name):
elements_and_names = engine.cube_parts.get(role_name, [])
for iris_object, cf_var_name in elements_and_names:
add_unused_attributes(iris_object, cf.cf_group[cf_var_name])
# Populate the attributes of all coordinates, cell-measures and ancillary-vars.
fix_attributes_all_elements("coordinates")
fix_attributes_all_elements("ancillary_variables")
fix_attributes_all_elements("cell_measures")
# Also populate attributes of the top-level cube itself.
add_unused_attributes(cube, cf_var)
# Work out reference names for all the coords.
names = {
coord.var_name: coord.standard_name or coord.var_name or "unknown"
for coord in cube.coords()
}
# Add all the cube cell methods.
cube.cell_methods = [
iris.coords.CellMethod(
method=method.method,
intervals=method.intervals,
comments=method.comments,
coords=[
names[coord_name] if coord_name in names else coord_name
for coord_name in method.coord_names
],
)
for method in cube.cell_methods
]
if DEBUG:
# Show activation statistics for this data-var (i.e. cube).
_actions_activation_stats(engine, cf_var.cf_name)
return cube
def _load_aux_factory(engine, cube):
"""
Convert any CF-netCDF dimensionless coordinate to an AuxCoordFactory.
"""
formula_type = engine.requires.get("formula_type")
if formula_type in [
"atmosphere_sigma_coordinate",
"atmosphere_hybrid_height_coordinate",
"atmosphere_hybrid_sigma_pressure_coordinate",
"ocean_sigma_z_coordinate",
"ocean_sigma_coordinate",
"ocean_s_coordinate",
"ocean_s_coordinate_g1",
"ocean_s_coordinate_g2",
]:
def coord_from_term(term):
# Convert term names to coordinates (via netCDF variable names).
name = engine.requires["formula_terms"].get(term, None)
if name is not None:
for coord, cf_var_name in engine.cube_parts["coordinates"]:
if cf_var_name == name:
return coord
warnings.warn(
"Unable to find coordinate for variable "
"{!r}".format(name)
)
if formula_type == "atmosphere_sigma_coordinate":
pressure_at_top = coord_from_term("ptop")
sigma = coord_from_term("sigma")
surface_air_pressure = coord_from_term("ps")
factory = AtmosphereSigmaFactory(
pressure_at_top, sigma, surface_air_pressure
)
elif formula_type == "atmosphere_hybrid_height_coordinate":
delta = coord_from_term("a")
sigma = coord_from_term("b")
orography = coord_from_term("orog")
factory = HybridHeightFactory(delta, sigma, orography)
elif formula_type == "atmosphere_hybrid_sigma_pressure_coordinate":
# Hybrid pressure has two valid versions of its formula terms:
# "p0: var1 a: var2 b: var3 ps: var4" or
# "ap: var1 b: var2 ps: var3" where "ap = p0 * a"
# Attempt to get the "ap" term.
delta = coord_from_term("ap")
if delta is None:
# The "ap" term is unavailable, so try getting terms "p0"
# and "a" terms in order to derive an "ap" equivalent term.
coord_p0 = coord_from_term("p0")
if coord_p0 is not None:
if coord_p0.shape != (1,):
msg = (
"Expecting {!r} to be a scalar reference "
"pressure coordinate, got shape {!r}".format(
coord_p0.var_name, coord_p0.shape
)
)
raise ValueError(msg)
if coord_p0.has_bounds():
msg = (
"Ignoring atmosphere hybrid sigma pressure "
"scalar coordinate {!r} bounds.".format(
coord_p0.name()
)
)
warnings.warn(msg)
coord_a = coord_from_term("a")
if coord_a is not None:
if coord_a.units.is_unknown():
# Be graceful, and promote unknown to dimensionless units.
coord_a.units = "1"
delta = coord_a * coord_p0.points[0]
delta.units = coord_a.units * coord_p0.units
delta.rename("vertical pressure")
delta.var_name = "ap"
cube.add_aux_coord(delta, cube.coord_dims(coord_a))
sigma = coord_from_term("b")
surface_air_pressure = coord_from_term("ps")
factory = HybridPressureFactory(delta, sigma, surface_air_pressure)
elif formula_type == "ocean_sigma_z_coordinate":
sigma = coord_from_term("sigma")
eta = coord_from_term("eta")
depth = coord_from_term("depth")
depth_c = coord_from_term("depth_c")
nsigma = coord_from_term("nsigma")
zlev = coord_from_term("zlev")
factory = OceanSigmaZFactory(
sigma, eta, depth, depth_c, nsigma, zlev
)
elif formula_type == "ocean_sigma_coordinate":
sigma = coord_from_term("sigma")
eta = coord_from_term("eta")
depth = coord_from_term("depth")
factory = OceanSigmaFactory(sigma, eta, depth)
elif formula_type == "ocean_s_coordinate":
s = coord_from_term("s")
eta = coord_from_term("eta")
depth = coord_from_term("depth")
a = coord_from_term("a")
depth_c = coord_from_term("depth_c")
b = coord_from_term("b")
factory = OceanSFactory(s, eta, depth, a, b, depth_c)
elif formula_type == "ocean_s_coordinate_g1":
s = coord_from_term("s")
c = coord_from_term("c")
eta = coord_from_term("eta")
depth = coord_from_term("depth")
depth_c = coord_from_term("depth_c")
factory = OceanSg1Factory(s, c, eta, depth, depth_c)
elif formula_type == "ocean_s_coordinate_g2":
s = coord_from_term("s")
c = coord_from_term("c")
eta = coord_from_term("eta")
depth = coord_from_term("depth")
depth_c = coord_from_term("depth_c")
factory = OceanSg2Factory(s, c, eta, depth, depth_c)
cube.add_aux_factory(factory)
def _translate_constraints_to_var_callback(constraints):
"""
Translate load constraints into a simple data-var filter function, if possible.
Returns:
* function(cf_var:CFDataVariable): --> bool,
or None.
For now, ONLY handles a single NameConstraint with no 'STASH' component.
"""
import iris._constraints
constraints = iris._constraints.list_of_constraints(constraints)
result = None
if len(constraints) == 1:
(constraint,) = constraints
if (
isinstance(constraint, iris._constraints.NameConstraint)
and constraint.STASH == "none"
):
# As long as it doesn't use a STASH match, then we can treat it as
# a testing against name properties of cf_var.
# That's just like testing against name properties of a cube, except that they may not all exist.
def inner(cf_datavar):
match = True
for name in constraint._names:
expected = getattr(constraint, name)
if name != "STASH" and expected != "none":
attr_name = "cf_name" if name == "var_name" else name
# Fetch property : N.B. CFVariable caches the property values
# The use of a default here is the only difference from the code in NameConstraint.
if not hasattr(cf_datavar, attr_name):
continue
actual = getattr(cf_datavar, attr_name, "")
if actual != expected:
match = False
break
return match
result = inner
return result
[docs]def load_cubes(filenames, callback=None, constraints=None):
"""
Loads cubes from a list of NetCDF filenames/URLs.
Args:
* filenames (string/list):
One or more NetCDF filenames/DAP URLs to load from.
Kwargs:
* callback (callable function):
Function which can be passed on to :func:`iris.io.run_callback`.
Returns:
Generator of loaded NetCDF :class:`iris.cubes.Cube`.
"""
from iris.io import run_callback
# Create a low-level data-var filter from the original load constraints, if they are suitable.
var_callback = _translate_constraints_to_var_callback(constraints)
# Create an actions engine.
engine = _actions_engine()
if isinstance(filenames, str):
filenames = [filenames]
for filename in filenames:
# Ingest the netCDF file.
cf = iris.fileformats.cf.CFReader(filename)
# Process each CF data variable.
data_variables = list(cf.cf_group.data_variables.values()) + list(
cf.cf_group.promoted.values()
)
for cf_var in data_variables:
if var_callback and not var_callback(cf_var):
# Deliver only selected results.
continue
cube = _load_cube(engine, cf, cf_var, filename)
# Process any associated formula terms and attach
# the corresponding AuxCoordFactory.
try:
_load_aux_factory(engine, cube)
except ValueError as e:
warnings.warn("{}".format(e))
# Perform any user registered callback function.
cube = run_callback(callback, cube, cf_var, filename)
# Callback mechanism may return None, which must not be yielded
if cube is None:
continue
yield cube
def _bytes_if_ascii(string):
"""
Convert the given string to a byte string (str in py2k, bytes in py3k)
if the given string can be encoded to ascii, else maintain the type
of the inputted string.
Note: passing objects without an `encode` method (such as None) will
be returned by the function unchanged.
"""
if isinstance(string, str):
try:
return string.encode(encoding="ascii")
except (AttributeError, UnicodeEncodeError):
pass
return string
def _setncattr(variable, name, attribute):
"""
Put the given attribute on the given netCDF4 Data type, casting
attributes as we go to bytes rather than unicode.
"""
attribute = _bytes_if_ascii(attribute)
return variable.setncattr(name, attribute)
class _FillValueMaskCheckAndStoreTarget:
"""
To be used with da.store. Remembers whether any element was equal to a
given value and whether it was masked, before passing the chunk to the
given target.
"""
def __init__(self, target, fill_value=None):
self.target = target
self.fill_value = fill_value
self.contains_value = False
self.is_masked = False
def __setitem__(self, keys, arr):
if self.fill_value is not None:
self.contains_value = self.contains_value or self.fill_value in arr
self.is_masked = self.is_masked or ma.is_masked(arr)
self.target[keys] = arr
[docs]class Saver:
"""A manager for saving netcdf files."""
def __init__(self, filename, netcdf_format):
"""
A manager for saving netcdf files.
Args:
* filename (string):
Name of the netCDF file to save the cube.
* netcdf_format (string):
Underlying netCDF file format, one of 'NETCDF4', 'NETCDF4_CLASSIC',
'NETCDF3_CLASSIC' or 'NETCDF3_64BIT'. Default is 'NETCDF4' format.
Returns:
None.
For example::
# Initialise Manager for saving
with Saver(filename, netcdf_format) as sman:
# Iterate through the cubelist.
for cube in cubes:
sman.write(cube)
"""
if netcdf_format not in [
"NETCDF4",
"NETCDF4_CLASSIC",
"NETCDF3_CLASSIC",
"NETCDF3_64BIT",
]:
raise ValueError(
"Unknown netCDF file format, got %r" % netcdf_format
)
# All persistent variables
#: CF name mapping with iris coordinates
self._name_coord_map = CFNameCoordMap()
#: List of dimension coordinates added to the file
self._dim_coords = []
#: List of grid mappings added to the file
self._coord_systems = []
#: A dictionary, listing dimension names and corresponding length
self._existing_dim = {}
#: A dictionary, mapping formula terms to owner cf variable name
self._formula_terms_cache = {}
#: NetCDF dataset
try:
self._dataset = netCDF4.Dataset(
filename, mode="w", format=netcdf_format
)
except RuntimeError:
dir_name = os.path.dirname(filename)
if not os.path.isdir(dir_name):
msg = "No such file or directory: {}".format(dir_name)
raise IOError(msg)
if not os.access(dir_name, os.R_OK | os.W_OK):
msg = "Permission denied: {}".format(filename)
raise IOError(msg)
else:
raise
def __enter__(self):
return self
[docs] def __exit__(self, type, value, traceback):
"""Flush any buffered data to the CF-netCDF file before closing."""
self._dataset.sync()
self._dataset.close()
[docs] def write(
self,
cube,
local_keys=None,
unlimited_dimensions=None,
zlib=False,
complevel=4,
shuffle=True,
fletcher32=False,
contiguous=False,
chunksizes=None,
endian="native",
least_significant_digit=None,
packing=None,
fill_value=None,
):
"""
Wrapper for saving cubes to a NetCDF file.
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
Kwargs:
* local_keys (iterable of strings):
An interable of cube attribute keys. Any cube attributes with
matching keys will become attributes on the data variable rather
than global attributes.
* unlimited_dimensions (iterable of strings and/or
:class:`iris.coords.Coord` objects):
List of coordinate names (or coordinate objects)
corresponding to coordinate dimensions of `cube` to save with the
NetCDF dimension variable length 'UNLIMITED'. By default, no
unlimited dimensions are saved. Only the 'NETCDF4' format
supports multiple 'UNLIMITED' dimensions.
* zlib (bool):
If `True`, the data will be compressed in the netCDF file using
gzip compression (default `False`).
* complevel (int):
An integer between 1 and 9 describing the level of compression
desired (default 4). Ignored if `zlib=False`.
* shuffle (bool):
If `True`, the HDF5 shuffle filter will be applied before
compressing the data (default `True`). This significantly improves
compression. Ignored if `zlib=False`.
* fletcher32 (bool):
If `True`, the Fletcher32 HDF5 checksum algorithm is activated to
detect errors. Default `False`.
* contiguous (bool):
If `True`, the variable data is stored contiguously on disk.
Default `False`. Setting to `True` for a variable with an unlimited
dimension will trigger an error.
* chunksizes (tuple of int):
Used to manually specify the HDF5 chunksizes for each dimension of
the variable. A detailed discussion of HDF chunking and I/O
performance is available here:
https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/netcdf_perf_chunking.html.
Basically, you want the chunk size for each dimension to match
as closely as possible the size of the data block that users will
read from the file. `chunksizes` cannot be set if `contiguous=True`.
* endian (string):
Used to control whether the data is stored in little or big endian
format on disk. Possible values are 'little', 'big' or 'native'
(default). The library will automatically handle endian conversions
when the data is read, but if the data is always going to be read
on a computer with the opposite format as the one used to create
the file, there may be some performance advantage to be gained by
setting the endian-ness.
* least_significant_digit (int):
If `least_significant_digit` is specified, variable data will be
truncated (quantized). In conjunction with `zlib=True` this
produces 'lossy', but significantly more efficient compression. For
example, if `least_significant_digit=1`, data will be quantized
using `numpy.around(scale*data)/scale`, where `scale = 2**bits`,
and `bits` is determined so that a precision of 0.1 is retained (in
this case `bits=4`). From
http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml:
"least_significant_digit -- power of ten of the smallest decimal
place in unpacked data that is a reliable value". Default is
`None`, or no quantization, or 'lossless' compression.
* packing (type or string or dict or list): A numpy integer datatype
(signed or unsigned) or a string that describes a numpy integer
dtype(i.e. 'i2', 'short', 'u4') or a dict of packing parameters as
described below. This provides support for netCDF data packing as
described in
https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/best_practices.html#bp_Packed-Data-Values
If this argument is a type (or type string), appropriate values of
scale_factor and add_offset will be automatically calculated based
on `cube.data` and possible masking. For more control, pass a dict
with one or more of the following keys: `dtype` (required),
`scale_factor` and `add_offset`. Note that automatic calculation of
packing parameters will trigger loading of lazy data; set them
manually using a dict to avoid this. The default is `None`, in
which case the datatype is determined from the cube and no packing
will occur.
* fill_value:
The value to use for the `_FillValue` attribute on the netCDF
variable. If `packing` is specified the value of `fill_value`
should be in the domain of the packed data.
Returns:
None.
.. note::
The `zlib`, `complevel`, `shuffle`, `fletcher32`, `contiguous`,
`chunksizes` and `endian` keywords are silently ignored for netCDF
3 files that do not use HDF5.
"""
if unlimited_dimensions is None:
unlimited_dimensions = []
cf_profile_available = iris.site_configuration.get(
"cf_profile"
) not in [None, False]
if cf_profile_available:
# Perform a CF profile of the cube. This may result in an exception
# being raised if mandatory requirements are not satisfied.
profile = iris.site_configuration["cf_profile"](cube)
# Ensure that attributes are CF compliant and if possible to make them
# compliant.
self.check_attribute_compliance(cube, cube.lazy_data())
for coord in cube.coords():
self.check_attribute_compliance(coord, coord.points)
# Get suitable dimension names.
dimension_names = self._get_dim_names(cube)
# Create the CF-netCDF data dimensions.
self._create_cf_dimensions(cube, dimension_names, unlimited_dimensions)
# Create the associated cube CF-netCDF data variable.
cf_var_cube = self._create_cf_data_variable(
cube,
dimension_names,
local_keys,
zlib=zlib,
complevel=complevel,
shuffle=shuffle,
fletcher32=fletcher32,
contiguous=contiguous,
chunksizes=chunksizes,
endian=endian,
least_significant_digit=least_significant_digit,
packing=packing,
fill_value=fill_value,
)
# Add coordinate variables.
self._add_dim_coords(cube, dimension_names)
# Add the auxiliary coordinate variables and associate the data
# variable to them
self._add_aux_coords(cube, cf_var_cube, dimension_names)
# Add the cell_measures variables and associate the data
# variable to them
self._add_cell_measures(cube, cf_var_cube, dimension_names)
# Add the ancillary_variables variables and associate the data variable
# to them
self._add_ancillary_variables(cube, cf_var_cube, dimension_names)
# Add the formula terms to the appropriate cf variables for each
# aux factory in the cube.
self._add_aux_factories(cube, cf_var_cube, dimension_names)
# Add data variable-only attribute names to local_keys.
if local_keys is None:
local_keys = set()
else:
local_keys = set(local_keys)
local_keys.update(_CF_DATA_ATTRS, _UKMO_DATA_ATTRS)
# Add global attributes taking into account local_keys.
global_attributes = {
k: v
for k, v in cube.attributes.items()
if (k not in local_keys and k.lower() != "conventions")
}
self.update_global_attributes(global_attributes)
if cf_profile_available:
cf_patch = iris.site_configuration.get("cf_patch")
if cf_patch is not None:
# Perform a CF patch of the dataset.
cf_patch(profile, self._dataset, cf_var_cube)
else:
msg = "cf_profile is available but no {} defined.".format(
"cf_patch"
)
warnings.warn(msg)
[docs] @staticmethod
def check_attribute_compliance(container, data):
def _coerce_value(val_attr, val_attr_value, data_dtype):
val_attr_tmp = np.array(val_attr_value, dtype=data_dtype)
if (val_attr_tmp != val_attr_value).any():
msg = '"{}" is not of a suitable value ({})'
raise ValueError(msg.format(val_attr, val_attr_value))
return val_attr_tmp
data_dtype = data.dtype
# Ensure that conflicting attributes are not provided.
if (
container.attributes.get("valid_min") is not None
or container.attributes.get("valid_max") is not None
) and container.attributes.get("valid_range") is not None:
msg = (
'Both "valid_range" and "valid_min" or "valid_max" '
"attributes present."
)
raise ValueError(msg)
# Ensure correct datatype
for val_attr in ["valid_range", "valid_min", "valid_max"]:
val_attr_value = container.attributes.get(val_attr)
if val_attr_value is not None:
val_attr_value = np.asarray(val_attr_value)
if data_dtype.itemsize == 1:
# Allow signed integral type
if val_attr_value.dtype.kind == "i":
continue
new_val = _coerce_value(val_attr, val_attr_value, data_dtype)
container.attributes[val_attr] = new_val
[docs] def update_global_attributes(self, attributes=None, **kwargs):
"""
Update the CF global attributes based on the provided
iterable/dictionary and/or keyword arguments.
Args:
* attributes (dict or iterable of key, value pairs):
CF global attributes to be updated.
"""
if attributes is not None:
# Handle sequence e.g. [('fruit', 'apple'), ...].
if not hasattr(attributes, "keys"):
attributes = dict(attributes)
for attr_name in sorted(attributes):
_setncattr(self._dataset, attr_name, attributes[attr_name])
for attr_name in sorted(kwargs):
_setncattr(self._dataset, attr_name, kwargs[attr_name])
def _create_cf_dimensions(
self, cube, dimension_names, unlimited_dimensions=None
):
"""
Create the CF-netCDF data dimensions.
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` in which to lookup coordinates.
Kwargs:
* unlimited_dimensions (iterable of strings and/or
:class:`iris.coords.Coord` objects):
List of coordinates to make unlimited (None by default).
Returns:
None.
"""
unlimited_dim_names = []
for coord in unlimited_dimensions:
try:
coord = cube.coord(name_or_coord=coord, dim_coords=True)
except iris.exceptions.CoordinateNotFoundError:
# coordinate isn't used for this cube, but it might be
# used for a different one
pass
else:
dim_name = self._get_coord_variable_name(cube, coord)
unlimited_dim_names.append(dim_name)
for dim_name in dimension_names:
if dim_name not in self._dataset.dimensions:
if dim_name in unlimited_dim_names:
size = None
else:
size = self._existing_dim[dim_name]
self._dataset.createDimension(dim_name, size)
def _add_inner_related_vars(
self,
cube,
cf_var_cube,
dimension_names,
coordlike_elements,
saver_create_method,
role_attribute_name,
):
# Common method to create a set of file variables and attach them to
# the parent data variable.
element_names = []
# Add CF-netCDF variables for the associated auxiliary coordinates.
for element in sorted(
coordlike_elements, key=lambda element: element.name()
):
# Create the associated CF-netCDF variable.
if element not in self._name_coord_map.coords:
cf_name = saver_create_method(cube, dimension_names, element)
self._name_coord_map.append(cf_name, element)
else:
cf_name = self._name_coord_map.name(element)
if cf_name is not None:
if role_attribute_name == "cell_measures":
# In the case of cell-measures, the attribute entries are not just
# a var_name, but each have the form "<measure>: <varname>".
cf_name = "{}: {}".format(element.measure, cf_name)
element_names.append(cf_name)
# Add CF-netCDF references to the primary data variable.
if element_names:
variable_names = " ".join(sorted(element_names))
_setncattr(cf_var_cube, role_attribute_name, variable_names)
def _add_aux_coords(self, cube, cf_var_cube, dimension_names):
"""
Add aux. coordinate to the dataset and associate with the data variable
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
* cf_var_cube (:class:`netcdf.netcdf_variable`):
cf variable cube representation.
* dimension_names (list):
Names associated with the dimensions of the cube.
"""
return self._add_inner_related_vars(
cube,
cf_var_cube,
dimension_names,
cube.aux_coords,
self._create_cf_coord_variable,
"coordinates",
)
def _add_cell_measures(self, cube, cf_var_cube, dimension_names):
"""
Add cell measures to the dataset and associate with the data variable
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
* cf_var_cube (:class:`netcdf.netcdf_variable`):
cf variable cube representation.
* dimension_names (list):
Names associated with the dimensions of the cube.
"""
return self._add_inner_related_vars(
cube,
cf_var_cube,
dimension_names,
cube.cell_measures(),
self._create_cf_cell_measure_variable,
"cell_measures",
)
def _add_ancillary_variables(self, cube, cf_var_cube, dimension_names):
"""
Add ancillary variables measures to the dataset and associate with the
data variable
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
* cf_var_cube (:class:`netcdf.netcdf_variable`):
cf variable cube representation.
* dimension_names (list):
Names associated with the dimensions of the cube.
"""
return self._add_inner_related_vars(
cube,
cf_var_cube,
dimension_names,
cube.ancillary_variables(),
self._create_cf_ancildata_variable,
"ancillary_variables",
)
def _add_dim_coords(self, cube, dimension_names):
"""
Add coordinate variables to NetCDF dataset.
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
* dimension_names (list):
Names associated with the dimensions of the cube.
"""
# Ensure we create the netCDF coordinate variables first.
for coord in cube.dim_coords:
# Create the associated coordinate CF-netCDF variable.
if coord not in self._name_coord_map.coords:
cf_name = self._create_cf_coord_variable(
cube, dimension_names, coord
)
self._name_coord_map.append(cf_name, coord)
def _add_aux_factories(self, cube, cf_var_cube, dimension_names):
"""
Modifies the variables of the NetCDF dataset to represent
the presence of dimensionless vertical coordinates based on
the aux factories of the cube (if any).
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
* cf_var_cube (:class:`netcdf.netcdf_variable`)
CF variable cube representation.
* dimension_names (list):
Names associated with the dimensions of the cube.
"""
primaries = []
for factory in cube.aux_factories:
factory_defn = _FACTORY_DEFNS.get(type(factory), None)
if factory_defn is None:
msg = (
"Unable to determine formula terms "
"for AuxFactory: {!r}".format(factory)
)
warnings.warn(msg)
else:
# Override `standard_name`, `long_name`, and `axis` of the
# primary coord that signals the presense of a dimensionless
# vertical coord, then set the `formula_terms` attribute.
primary_coord = factory.dependencies[factory_defn.primary]
if primary_coord in primaries:
msg = (
"Cube {!r} has multiple aux factories that share "
"a common primary coordinate {!r}. Unable to save "
"to netCDF as having multiple formula terms on a "
"single coordinate is not supported."
)
raise ValueError(msg.format(cube, primary_coord.name()))
primaries.append(primary_coord)
cf_name = self._name_coord_map.name(primary_coord)
cf_var = self._dataset.variables[cf_name]
names = {
key: self._name_coord_map.name(coord)
for key, coord in factory.dependencies.items()
}
formula_terms = factory_defn.formula_terms_format.format(
**names
)
std_name = factory_defn.std_name
if hasattr(cf_var, "formula_terms"):
if (
cf_var.formula_terms != formula_terms
or cf_var.standard_name != std_name
):
# TODO: We need to resolve this corner-case where
# the dimensionless vertical coordinate containing the
# formula_terms is a dimension coordinate of the
# associated cube and a new alternatively named
# dimensionless vertical coordinate is required with
# new formula_terms and a renamed dimension.
if cf_name in dimension_names:
msg = (
"Unable to create dimensonless vertical "
"coordinate."
)
raise ValueError(msg)
key = (cf_name, std_name, formula_terms)
name = self._formula_terms_cache.get(key)
if name is None:
# Create a new variable
name = self._create_cf_coord_variable(
cube, dimension_names, primary_coord
)
cf_var = self._dataset.variables[name]
_setncattr(cf_var, "standard_name", std_name)
_setncattr(cf_var, "axis", "Z")
# Update the formula terms.
ft = formula_terms.split()
ft = [name if t == cf_name else t for t in ft]
_setncattr(cf_var, "formula_terms", " ".join(ft))
# Update the cache.
self._formula_terms_cache[key] = name
# Update the associated cube variable.
coords = cf_var_cube.coordinates.split()
coords = [name if c == cf_name else c for c in coords]
_setncattr(
cf_var_cube, "coordinates", " ".join(coords)
)
else:
_setncattr(cf_var, "standard_name", std_name)
_setncattr(cf_var, "axis", "Z")
_setncattr(cf_var, "formula_terms", formula_terms)
def _get_dim_names(self, cube):
"""
Determine suitable CF-netCDF data dimension names.
Args:
* cube (:class:`iris.cube.Cube`):
A :class:`iris.cube.Cube` to be saved to a netCDF file.
Returns:
List of dimension names with length equal the number of dimensions
in the cube.
"""
dimension_names = []
for dim in range(cube.ndim):
coords = cube.coords(dimensions=dim, dim_coords=True)
if coords:
coord = coords[0]
dim_name = self._get_coord_variable_name(cube, coord)
# Add only dimensions that have not already been added.
if coord not in self._dim_coords:
# Determine unique dimension name
while (
dim_name in self._existing_dim
or dim_name in self._name_coord_map.names
):
dim_name = self._increment_name(dim_name)
# Update names added, current cube dim names used and
# unique coordinates added.
self._existing_dim[dim_name] = coord.shape[0]
dimension_names.append(dim_name)
self._dim_coords.append(coord)
else:
# Return the dim_name associated with the existing
# coordinate.
dim_name = self._name_coord_map.name(coord)
dimension_names.append(dim_name)
else:
# No CF-netCDF coordinates describe this data dimension.
dim_name = "dim%d" % dim
if dim_name in self._existing_dim:
# Increment name if conflicted with one already existing.
if self._existing_dim[dim_name] != cube.shape[dim]:
while (
dim_name in self._existing_dim
and self._existing_dim[dim_name] != cube.shape[dim]
or dim_name in self._name_coord_map.names
):
dim_name = self._increment_name(dim_name)
# Update dictionary with new entry
self._existing_dim[dim_name] = cube.shape[dim]
else:
# Update dictionary with new entry
self._existing_dim[dim_name] = cube.shape[dim]
dimension_names.append(dim_name)
return dimension_names
[docs] @staticmethod
def cf_valid_var_name(var_name):
"""
Return a valid CF var_name given a potentially invalid name.
Args:
* var_name (str):
The var_name to normalise
Returns:
A var_name suitable for passing through for variable creation.
"""
# Replace invalid charaters with an underscore ("_").
var_name = re.sub(r"[^a-zA-Z0-9]", "_", var_name)
# Ensure the variable name starts with a letter.
if re.match(r"^[^a-zA-Z]", var_name):
var_name = "var_{}".format(var_name)
return var_name
@staticmethod
def _cf_coord_identity(coord):
"""
Determine a suitable units from a given coordinate.
Args:
* coord (:class:`iris.coords.Coord`):
A coordinate of a cube.
Returns:
The (standard_name, long_name, unit) of the given
:class:`iris.coords.Coord` instance.
"""
units = str(coord.units)
# Set the 'units' of 'latitude' and 'longitude' coordinates specified
# in 'degrees' to 'degrees_north' and 'degrees_east' respectively,
# as defined in the CF conventions for netCDF files: sections 4.1 and
# 4.2.
if (
isinstance(coord.coord_system, iris.coord_systems.GeogCS)
or coord.coord_system is None
) and coord.units == "degrees":
if coord.standard_name == "latitude":
units = "degrees_north"
elif coord.standard_name == "longitude":
units = "degrees_east"
return coord.standard_name, coord.long_name, units
def _ensure_valid_dtype(self, values, src_name, src_object):
# NetCDF3 and NetCDF4 classic do not support int64 or unsigned ints,
# so we check if we can store them as int32 instead.
if (
np.issubdtype(values.dtype, np.int64)
or np.issubdtype(values.dtype, np.unsignedinteger)
) and self._dataset.file_format in (
"NETCDF3_CLASSIC",
"NETCDF3_64BIT",
"NETCDF4_CLASSIC",
):
# Cast to an integer type supported by netCDF3.
if not np.can_cast(values.max(), np.int32) or not np.can_cast(
values.min(), np.int32
):
msg = (
"The data type of {} {!r} is not supported by {} and"
" its values cannot be safely cast to a supported"
" integer type."
)
msg = msg.format(
src_name, src_object, self._dataset.file_format
)
raise ValueError(msg)
values = values.astype(np.int32)
return values
def _create_cf_bounds(self, coord, cf_var, cf_name):
"""
Create the associated CF-netCDF bounds variable.
Args:
* coord (:class:`iris.coords.Coord`):
A coordinate of a cube.
* cf_var:
CF-netCDF variable
* cf_name (string):
name of the CF-NetCDF variable.
Returns:
None
"""
if coord.has_bounds():
# Get the values in a form which is valid for the file format.
bounds = self._ensure_valid_dtype(
coord.bounds, "the bounds of coordinate", coord
)
n_bounds = bounds.shape[-1]
if n_bounds == 2:
bounds_dimension_name = "bnds"
else:
bounds_dimension_name = "bnds_%s" % n_bounds
if coord.climatological:
property_name = "climatology"
varname_extra = "climatology"
else:
property_name = "bounds"
varname_extra = "bnds"
if bounds_dimension_name not in self._dataset.dimensions:
# Create the bounds dimension with the appropriate extent.
self._dataset.createDimension(bounds_dimension_name, n_bounds)
boundsvar_name = "{}_{}".format(cf_name, varname_extra)
_setncattr(cf_var, property_name, boundsvar_name)
cf_var_bounds = self._dataset.createVariable(
boundsvar_name,
bounds.dtype.newbyteorder("="),
cf_var.dimensions + (bounds_dimension_name,),
)
cf_var_bounds[:] = bounds
def _get_cube_variable_name(self, cube):
"""
Returns a CF-netCDF variable name for the given cube.
Args:
* cube (class:`iris.cube.Cube`):
An instance of a cube for which a CF-netCDF variable
name is required.
Returns:
A CF-netCDF variable name as a string.
"""
if cube.var_name is not None:
cf_name = cube.var_name
else:
# Convert to lower case and replace whitespace by underscores.
cf_name = "_".join(cube.name().lower().split())
cf_name = self.cf_valid_var_name(cf_name)
return cf_name
def _get_coord_variable_name(self, cube, coord):
"""
Returns a CF-netCDF variable name for the given coordinate.
Args:
* cube (:class:`iris.cube.Cube`):
The cube that contains the given coordinate.
* coord (:class:`iris.coords.Coord`):
An instance of a coordinate for which a CF-netCDF variable
name is required.
Returns:
A CF-netCDF variable name as a string.
"""
if coord.var_name is not None:
cf_name = coord.var_name
else:
name = coord.standard_name or coord.long_name
if not name or set(name).intersection(string.whitespace):
# Auto-generate name based on associated dimensions.
name = ""
for dim in cube.coord_dims(coord):
name += "dim{}".format(dim)
# Handle scalar coordinate (dims == ()).
if not name:
name = "unknown_scalar"
# Convert to lower case and replace whitespace by underscores.
cf_name = "_".join(name.lower().split())
cf_name = self.cf_valid_var_name(cf_name)
return cf_name
def _inner_create_cf_cellmeasure_or_ancil_variable(
self, cube, dimension_names, dimensional_metadata
):
"""
Create the associated CF-netCDF variable in the netCDF dataset for the
given dimensional_metadata.
Args:
* cube (:class:`iris.cube.Cube`):
The associated cube being saved to CF-netCDF file.
* dimension_names (list):
Names for each dimension of the cube.
* dimensional_metadata (:class:`iris.coords.CellMeasure`):
A cell measure OR ancillary variable to be saved to the
CF-netCDF file.
In either case, provides data, units and standard/long/var names.
Returns:
The string name of the associated CF-netCDF variable saved.
"""
cf_name = self._get_coord_variable_name(cube, dimensional_metadata)
while cf_name in self._dataset.variables:
cf_name = self._increment_name(cf_name)
# Derive the data dimension names for the coordinate.
cf_dimensions = [
dimension_names[dim]
for dim in dimensional_metadata.cube_dims(cube)
]
# Get the data values.
data = dimensional_metadata.data
if isinstance(dimensional_metadata, iris.coords.CellMeasure):
# Disallow saving of *masked* cell measures.
# NOTE: currently, this is the only functional difference required
# between variable creation for an ancillary and a cell measure.
if ma.is_masked(data):
# We can't save masked points properly, as we don't maintain a
# suitable fill_value. (Load will not record one, either).
msg = "Cell measures with missing data are not supported."
raise ValueError(msg)
# Get the values in a form which is valid for the file format.
data = self._ensure_valid_dtype(
data, "coordinate", dimensional_metadata
)
# Create the CF-netCDF variable.
cf_var = self._dataset.createVariable(
cf_name, data.dtype.newbyteorder("="), cf_dimensions
)
# Add the data to the CF-netCDF variable.
cf_var[:] = data
if dimensional_metadata.units.is_udunits():
_setncattr(cf_var, "units", str(dimensional_metadata.units))
if dimensional_metadata.standard_name is not None:
_setncattr(
cf_var, "standard_name", dimensional_metadata.standard_name
)
if dimensional_metadata.long_name is not None:
_setncattr(cf_var, "long_name", dimensional_metadata.long_name)
# Add any other custom coordinate attributes.
for name in sorted(dimensional_metadata.attributes):
value = dimensional_metadata.attributes[name]
# Don't clobber existing attributes.
if not hasattr(cf_var, name):
_setncattr(cf_var, name, value)
return cf_name
def _create_cf_cell_measure_variable(
self, cube, dimension_names, cell_measure
):
"""
Create the associated CF-netCDF variable in the netCDF dataset for the
given cell_measure.
Args:
* cube (:class:`iris.cube.Cube`):
The associated cube being saved to CF-netCDF file.
* dimension_names (list):
Names for each dimension of the cube.
* cell_measure (:class:`iris.coords.CellMeasure`):
The cell measure to be saved to CF-netCDF file.
Returns:
The string name of the associated CF-netCDF variable saved.
"""
# Note: currently shares variable creation code with ancillary-variables.
return self._inner_create_cf_cellmeasure_or_ancil_variable(
cube, dimension_names, cell_measure
)
def _create_cf_ancildata_variable(
self, cube, dimension_names, ancillary_variable
):
"""
Create the associated CF-netCDF variable in the netCDF dataset for the
given ancillary variable.
Args:
* cube (:class:`iris.cube.Cube`):
The associated cube being saved to CF-netCDF file.
* dimension_names (list):
Names for each dimension of the cube.
* ancillary_variable (:class:`iris.coords.AncillaryVariable`):
The ancillary variable to be saved to the CF-netCDF file.
Returns:
The string name of the associated CF-netCDF variable saved.
"""
# Note: currently shares variable creation code with cell-measures.
return self._inner_create_cf_cellmeasure_or_ancil_variable(
cube, dimension_names, ancillary_variable
)
def _create_cf_coord_variable(self, cube, dimension_names, coord):
"""
Create the associated CF-netCDF variable in the netCDF dataset for the
given coordinate. If required, also create the CF-netCDF bounds
variable and associated dimension.
Args:
* cube (:class:`iris.cube.Cube`):
The associated cube being saved to CF-netCDF file.
* dimension_names (list):
Names for each dimension of the cube.
* coord (:class:`iris.coords.Coord`):
The coordinate to be saved to CF-netCDF file.
Returns:
The string name of the associated CF-netCDF variable saved.
"""
cf_name = self._get_coord_variable_name(cube, coord)
while cf_name in self._dataset.variables:
cf_name = self._increment_name(cf_name)
# Derive the data dimension names for the coordinate.
cf_dimensions = [
dimension_names[dim] for dim in cube.coord_dims(coord)
]
if np.issubdtype(coord.points.dtype, np.str_):
string_dimension_depth = coord.points.dtype.itemsize
if coord.points.dtype.kind == "U":
string_dimension_depth //= 4
string_dimension_name = "string%d" % string_dimension_depth
# Determine whether to create the string length dimension.
if string_dimension_name not in self._dataset.dimensions:
self._dataset.createDimension(
string_dimension_name, string_dimension_depth
)
# Add the string length dimension to dimension names.
cf_dimensions.append(string_dimension_name)
# Create the label coordinate variable.
cf_var = self._dataset.createVariable(
cf_name, "|S1", cf_dimensions
)
# Add the payload to the label coordinate variable.
if len(cf_dimensions) == 1:
cf_var[:] = list(
"%- *s" % (string_dimension_depth, coord.points[0])
)
else:
for index in np.ndindex(coord.points.shape):
index_slice = tuple(list(index) + [slice(None, None)])
cf_var[index_slice] = list(
"%- *s" % (string_dimension_depth, coord.points[index])
)
else:
# Identify the collection of coordinates that represent CF-netCDF
# coordinate variables.
cf_coordinates = cube.dim_coords
if coord in cf_coordinates:
# By definition of a CF-netCDF coordinate variable this
# coordinate must be 1-D and the name of the CF-netCDF variable
# must be the same as its dimension name.
cf_name = cf_dimensions[0]
# Get the values in a form which is valid for the file format.
points = self._ensure_valid_dtype(
coord.points, "coordinate", coord
)
# Create the CF-netCDF variable.
cf_var = self._dataset.createVariable(
cf_name, points.dtype.newbyteorder("="), cf_dimensions
)
# Add the axis attribute for spatio-temporal CF-netCDF coordinates.
if coord in cf_coordinates:
axis = iris.util.guess_coord_axis(coord)
if axis is not None and axis.lower() in SPATIO_TEMPORAL_AXES:
_setncattr(cf_var, "axis", axis.upper())
# Add the data to the CF-netCDF variable.
cf_var[:] = points
# Create the associated CF-netCDF bounds variable.
self._create_cf_bounds(coord, cf_var, cf_name)
# Deal with CF-netCDF units and standard name.
standard_name, long_name, units = self._cf_coord_identity(coord)
if cf_units.as_unit(units).is_udunits():
_setncattr(cf_var, "units", units)
if standard_name is not None:
_setncattr(cf_var, "standard_name", standard_name)
if long_name is not None:
_setncattr(cf_var, "long_name", long_name)
# Add the CF-netCDF calendar attribute.
if coord.units.calendar:
_setncattr(cf_var, "calendar", coord.units.calendar)
# Add any other custom coordinate attributes.
for name in sorted(coord.attributes):
value = coord.attributes[name]
if name == "STASH":
# Adopting provisional Metadata Conventions for representing MO
# Scientific Data encoded in NetCDF Format.
name = "um_stash_source"
value = str(value)
# Don't clobber existing attributes.
if not hasattr(cf_var, name):
_setncattr(cf_var, name, value)
return cf_name
def _create_cf_cell_methods(self, cube, dimension_names):
"""
Create CF-netCDF string representation of a cube cell methods.
Args:
* cube (:class:`iris.cube.Cube`) or cubelist
(:class:`iris.cube.CubeList`):
A :class:`iris.cube.Cube`, :class:`iris.cube.CubeList` or list of
cubes to be saved to a netCDF file.
* dimension_names (list):
Names associated with the dimensions of the cube.
Returns:
CF-netCDF string representation of a cube cell methods.
"""
cell_methods = []
# Identify the collection of coordinates that represent CF-netCDF
# coordinate variables.
cf_coordinates = cube.dim_coords
for cm in cube.cell_methods:
names = ""
for name in cm.coord_names:
coord = cube.coords(name)
if coord:
coord = coord[0]
if coord in cf_coordinates:
name = dimension_names[cube.coord_dims(coord)[0]]
names += "%s: " % name
interval = " ".join(
["interval: %s" % interval for interval in cm.intervals or []]
)
comment = " ".join(
["comment: %s" % comment for comment in cm.comments or []]
)
extra = " ".join([interval, comment]).strip()
if extra:
extra = " (%s)" % extra
cell_methods.append(names + cm.method + extra)
return " ".join(cell_methods)
def _create_cf_grid_mapping(self, cube, cf_var_cube):
"""
Create CF-netCDF grid mapping variable and associated CF-netCDF
data variable grid mapping attribute.
Args:
* cube (:class:`iris.cube.Cube`) or cubelist
(:class:`iris.cube.CubeList`):
A :class:`iris.cube.Cube`, :class:`iris.cube.CubeList` or list of
cubes to be saved to a netCDF file.
* cf_var_cube (:class:`netcdf.netcdf_variable`):
cf variable cube representation.
Returns:
None
"""
cs = cube.coord_system("CoordSystem")
if cs is not None:
# Grid var not yet created?
if cs not in self._coord_systems:
while cs.grid_mapping_name in self._dataset.variables:
aname = self._increment_name(cs.grid_mapping_name)
cs.grid_mapping_name = aname
cf_var_grid = self._dataset.createVariable(
cs.grid_mapping_name, np.int32
)
_setncattr(
cf_var_grid, "grid_mapping_name", cs.grid_mapping_name
)
def add_ellipsoid(ellipsoid):
cf_var_grid.longitude_of_prime_meridian = (
ellipsoid.longitude_of_prime_meridian
)
semi_major = ellipsoid.semi_major_axis
semi_minor = ellipsoid.semi_minor_axis
if semi_minor == semi_major:
cf_var_grid.earth_radius = semi_major
else:
cf_var_grid.semi_major_axis = semi_major
cf_var_grid.semi_minor_axis = semi_minor
# latlon
if isinstance(cs, iris.coord_systems.GeogCS):
add_ellipsoid(cs)
# rotated latlon
elif isinstance(cs, iris.coord_systems.RotatedGeogCS):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.grid_north_pole_latitude = (
cs.grid_north_pole_latitude
)
cf_var_grid.grid_north_pole_longitude = (
cs.grid_north_pole_longitude
)
cf_var_grid.north_pole_grid_longitude = (
cs.north_pole_grid_longitude
)
# tmerc
elif isinstance(cs, iris.coord_systems.TransverseMercator):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_central_meridian = (
cs.longitude_of_central_meridian
)
cf_var_grid.latitude_of_projection_origin = (
cs.latitude_of_projection_origin
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
cf_var_grid.scale_factor_at_central_meridian = (
cs.scale_factor_at_central_meridian
)
# merc
elif isinstance(cs, iris.coord_systems.Mercator):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_projection_origin = (
cs.longitude_of_projection_origin
)
# The Mercator class has implicit defaults for certain
# parameters
cf_var_grid.false_easting = 0.0
cf_var_grid.false_northing = 0.0
cf_var_grid.scale_factor_at_projection_origin = 1.0
# lcc
elif isinstance(cs, iris.coord_systems.LambertConformal):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.standard_parallel = cs.secant_latitudes
cf_var_grid.latitude_of_projection_origin = cs.central_lat
cf_var_grid.longitude_of_central_meridian = cs.central_lon
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
# stereo
elif isinstance(cs, iris.coord_systems.Stereographic):
if cs.true_scale_lat is not None:
warnings.warn(
"Stereographic coordinate systems with "
"true scale latitude specified are not "
"yet handled"
)
else:
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_projection_origin = (
cs.central_lon
)
cf_var_grid.latitude_of_projection_origin = (
cs.central_lat
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
# The Stereographic class has an implicit scale
# factor
cf_var_grid.scale_factor_at_projection_origin = 1.0
# osgb (a specific tmerc)
elif isinstance(cs, iris.coord_systems.OSGB):
warnings.warn("OSGB coordinate system not yet handled")
# lambert azimuthal equal area
elif isinstance(
cs, iris.coord_systems.LambertAzimuthalEqualArea
):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_projection_origin = (
cs.longitude_of_projection_origin
)
cf_var_grid.latitude_of_projection_origin = (
cs.latitude_of_projection_origin
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
# albers conical equal area
elif isinstance(cs, iris.coord_systems.AlbersEqualArea):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_central_meridian = (
cs.longitude_of_central_meridian
)
cf_var_grid.latitude_of_projection_origin = (
cs.latitude_of_projection_origin
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
cf_var_grid.standard_parallel = cs.standard_parallels
# vertical perspective
elif isinstance(cs, iris.coord_systems.VerticalPerspective):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_projection_origin = (
cs.longitude_of_projection_origin
)
cf_var_grid.latitude_of_projection_origin = (
cs.latitude_of_projection_origin
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
cf_var_grid.perspective_point_height = (
cs.perspective_point_height
)
# geostationary
elif isinstance(cs, iris.coord_systems.Geostationary):
if cs.ellipsoid:
add_ellipsoid(cs.ellipsoid)
cf_var_grid.longitude_of_projection_origin = (
cs.longitude_of_projection_origin
)
cf_var_grid.latitude_of_projection_origin = (
cs.latitude_of_projection_origin
)
cf_var_grid.false_easting = cs.false_easting
cf_var_grid.false_northing = cs.false_northing
cf_var_grid.perspective_point_height = (
cs.perspective_point_height
)
cf_var_grid.sweep_angle_axis = cs.sweep_angle_axis
# other
else:
warnings.warn(
"Unable to represent the horizontal "
"coordinate system. The coordinate system "
"type %r is not yet implemented." % type(cs)
)
self._coord_systems.append(cs)
# Refer to grid var
_setncattr(cf_var_cube, "grid_mapping", cs.grid_mapping_name)
def _create_cf_data_variable(
self,
cube,
dimension_names,
local_keys=None,
packing=None,
fill_value=None,
**kwargs,
):
"""
Create CF-netCDF data variable for the cube and any associated grid
mapping.
Args:
* cube (:class:`iris.cube.Cube`):
The associated cube being saved to CF-netCDF file.
* dimension_names (list):
String names for each dimension of the cube.
Kwargs:
* local_keys (iterable of strings):
* see :func:`iris.fileformats.netcdf.Saver.write`
* packing (type or string or dict or list):
* see :func:`iris.fileformats.netcdf.Saver.write`
* fill_value:
* see :func:`iris.fileformats.netcdf.Saver.write`
All other keywords are passed through to the dataset's `createVariable`
method.
Returns:
The newly created CF-netCDF data variable.
"""
if packing:
if isinstance(packing, dict):
if "dtype" not in packing:
msg = "The dtype attribute is required for packing."
raise ValueError(msg)
dtype = np.dtype(packing["dtype"])
scale_factor = packing.get("scale_factor", None)
add_offset = packing.get("add_offset", None)
valid_keys = {"dtype", "scale_factor", "add_offset"}
invalid_keys = set(packing.keys()) - valid_keys
if invalid_keys:
msg = (
"Invalid packing key(s) found: '{}'. The valid "
"keys are '{}'.".format(
"', '".join(invalid_keys), "', '".join(valid_keys)
)
)
raise ValueError(msg)
else:
# We compute the scale_factor and add_offset based on the
# min/max of the data. This requires the data to be loaded.
masked = ma.isMaskedArray(cube.data)
dtype = np.dtype(packing)
cmax = cube.data.max()
cmin = cube.data.min()
n = dtype.itemsize * 8
if masked:
scale_factor = (cmax - cmin) / (2 ** n - 2)
else:
scale_factor = (cmax - cmin) / (2 ** n - 1)
if dtype.kind == "u":
add_offset = cmin
elif dtype.kind == "i":
if masked:
add_offset = (cmax + cmin) / 2
else:
add_offset = cmin + 2 ** (n - 1) * scale_factor
def set_packing_ncattrs(cfvar):
"""Set netCDF packing attributes."""
if packing:
if scale_factor:
_setncattr(cfvar, "scale_factor", scale_factor)
if add_offset:
_setncattr(cfvar, "add_offset", add_offset)
cf_name = self._get_cube_variable_name(cube)
while cf_name in self._dataset.variables:
cf_name = self._increment_name(cf_name)
# if netcdf3 avoid streaming due to dtype handling
if not cube.has_lazy_data() or self._dataset.file_format in (
"NETCDF3_CLASSIC",
"NETCDF3_64BIT",
):
# Get the values in a form which is valid for the file format.
data = self._ensure_valid_dtype(cube.data, "cube", cube)
def store(data, cf_var, fill_value):
cf_var[:] = data
is_masked = ma.is_masked(data)
contains_value = fill_value is not None and fill_value in data
return is_masked, contains_value
else:
data = cube.lazy_data()
def store(data, cf_var, fill_value):
# Store lazy data and check whether it is masked and contains
# the fill value
target = _FillValueMaskCheckAndStoreTarget(cf_var, fill_value)
da.store([data], [target])
return target.is_masked, target.contains_value
if not packing:
dtype = data.dtype.newbyteorder("=")
# Create the cube CF-netCDF data variable with data payload.
cf_var = self._dataset.createVariable(
cf_name, dtype, dimension_names, fill_value=fill_value, **kwargs
)
set_packing_ncattrs(cf_var)
# If packing attributes are specified, don't bother checking whether
# the fill value is in the data.
if packing:
fill_value_to_check = None
elif fill_value is not None:
fill_value_to_check = fill_value
else:
fill_value_to_check = netCDF4.default_fillvals[dtype.str[1:]]
# Store the data and check if it is masked and contains the fill value
is_masked, contains_fill_value = store(
data, cf_var, fill_value_to_check
)
if dtype.itemsize == 1 and fill_value is None:
if is_masked:
msg = (
"Cube '{}' contains byte data with masked points, but "
"no fill_value keyword was given. As saved, these "
"points will read back as valid values. To save as "
"masked byte data, please explicitly specify the "
"'fill_value' keyword."
)
warnings.warn(msg.format(cube.name()))
elif contains_fill_value:
msg = (
"Cube '{}' contains unmasked data points equal to the "
"fill-value, {}. As saved, these points will read back "
"as missing data. To save these as normal values, please "
"specify a 'fill_value' keyword not equal to any valid "
"data points."
)
warnings.warn(msg.format(cube.name(), fill_value))
if cube.standard_name:
_setncattr(cf_var, "standard_name", cube.standard_name)
if cube.long_name:
_setncattr(cf_var, "long_name", cube.long_name)
if cube.units.is_udunits():
_setncattr(cf_var, "units", str(cube.units))
# Add the CF-netCDF calendar attribute.
if cube.units.calendar:
_setncattr(cf_var, "calendar", cube.units.calendar)
# Add data variable-only attribute names to local_keys.
if local_keys is None:
local_keys = set()
else:
local_keys = set(local_keys)
local_keys.update(_CF_DATA_ATTRS, _UKMO_DATA_ATTRS)
# Add any cube attributes whose keys are in local_keys as
# CF-netCDF data variable attributes.
attr_names = set(cube.attributes).intersection(local_keys)
for attr_name in sorted(attr_names):
# Do not output 'conventions' attribute.
if attr_name.lower() == "conventions":
continue
value = cube.attributes[attr_name]
if attr_name == "STASH":
# Adopting provisional Metadata Conventions for representing MO
# Scientific Data encoded in NetCDF Format.
attr_name = "um_stash_source"
value = str(value)
if attr_name == "ukmo__process_flags":
value = " ".join([x.replace(" ", "_") for x in value])
if attr_name in _CF_GLOBAL_ATTRS:
msg = (
"{attr_name!r} is being added as CF data variable "
"attribute, but {attr_name!r} should only be a CF "
"global attribute.".format(attr_name=attr_name)
)
warnings.warn(msg)
_setncattr(cf_var, attr_name, value)
# Create the CF-netCDF data variable cell method attribute.
cell_methods = self._create_cf_cell_methods(cube, dimension_names)
if cell_methods:
_setncattr(cf_var, "cell_methods", cell_methods)
# Create the CF-netCDF grid mapping.
self._create_cf_grid_mapping(cube, cf_var)
return cf_var
def _increment_name(self, varname):
"""
Increment string name or begin increment.
Avoidance of conflicts between variable names, where the name is
incremented to distinguish it from others.
Args:
* varname (string):
Variable name to increment.
Returns:
Incremented varname.
"""
num = 0
try:
name, endnum = varname.rsplit("_", 1)
if endnum.isdigit():
num = int(endnum) + 1
varname = name
except ValueError:
pass
return "{}_{}".format(varname, num)
[docs]def save(
cube,
filename,
netcdf_format="NETCDF4",
local_keys=None,
unlimited_dimensions=None,
zlib=False,
complevel=4,
shuffle=True,
fletcher32=False,
contiguous=False,
chunksizes=None,
endian="native",
least_significant_digit=None,
packing=None,
fill_value=None,
):
"""
Save cube(s) to a netCDF file, given the cube and the filename.
* Iris will write CF 1.7 compliant NetCDF files.
* The attributes dictionaries on each cube in the saved cube list
will be compared and common attributes saved as NetCDF global
attributes where appropriate.
* Keyword arguments specifying how to save the data are applied
to each cube. To use different settings for different cubes, use
the NetCDF Context manager (:class:`~Saver`) directly.
* The save process will stream the data payload to the file using dask,
enabling large data payloads to be saved and maintaining the 'lazy'
status of the cube's data payload, unless the netcdf_format is explicitly
specified to be 'NETCDF3' or 'NETCDF3_CLASSIC'.
Args:
* cube (:class:`iris.cube.Cube` or :class:`iris.cube.CubeList`):
A :class:`iris.cube.Cube`, :class:`iris.cube.CubeList` or other
iterable of cubes to be saved to a netCDF file.
* filename (string):
Name of the netCDF file to save the cube(s).
Kwargs:
* netcdf_format (string):
Underlying netCDF file format, one of 'NETCDF4', 'NETCDF4_CLASSIC',
'NETCDF3_CLASSIC' or 'NETCDF3_64BIT'. Default is 'NETCDF4' format.
* local_keys (iterable of strings):
An interable of cube attribute keys. Any cube attributes with
matching keys will become attributes on the data variable rather
than global attributes.
* unlimited_dimensions (iterable of strings and/or
:class:`iris.coords.Coord` objects):
List of coordinate names (or coordinate objects) corresponding
to coordinate dimensions of `cube` to save with the NetCDF dimension
variable length 'UNLIMITED'. By default, no unlimited dimensions are
saved. Only the 'NETCDF4' format supports multiple 'UNLIMITED'
dimensions.
* zlib (bool):
If `True`, the data will be compressed in the netCDF file using gzip
compression (default `False`).
* complevel (int):
An integer between 1 and 9 describing the level of compression desired
(default 4). Ignored if `zlib=False`.
* shuffle (bool):
If `True`, the HDF5 shuffle filter will be applied before compressing
the data (default `True`). This significantly improves compression.
Ignored if `zlib=False`.
* fletcher32 (bool):
If `True`, the Fletcher32 HDF5 checksum algorithm is activated to
detect errors. Default `False`.
* contiguous (bool):
If `True`, the variable data is stored contiguously on disk. Default
`False`. Setting to `True` for a variable with an unlimited dimension
will trigger an error.
* chunksizes (tuple of int):
Used to manually specify the HDF5 chunksizes for each dimension of the
variable. A detailed discussion of HDF chunking and I/O performance is
available here: https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/netcdf_perf_chunking.html.
Basically, you want the chunk size for each dimension to match as
closely as possible the size of the data block that users will read
from the file. `chunksizes` cannot be set if `contiguous=True`.
* endian (string):
Used to control whether the data is stored in little or big endian
format on disk. Possible values are 'little', 'big' or 'native'
(default). The library will automatically handle endian conversions
when the data is read, but if the data is always going to be read on a
computer with the opposite format as the one used to create the file,
there may be some performance advantage to be gained by setting the
endian-ness.
* least_significant_digit (int):
If `least_significant_digit` is specified, variable data will be
truncated (quantized). In conjunction with `zlib=True` this produces
'lossy', but significantly more efficient compression. For example, if
`least_significant_digit=1`, data will be quantized using
`numpy.around(scale*data)/scale`, where `scale = 2**bits`, and `bits`
is determined so that a precision of 0.1 is retained (in this case
`bits=4`). From
http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml:
"least_significant_digit -- power of ten of the smallest decimal place
in unpacked data that is a reliable value". Default is `None`, or no
quantization, or 'lossless' compression.
* packing (type or string or dict or list): A numpy integer datatype
(signed or unsigned) or a string that describes a numpy integer dtype
(i.e. 'i2', 'short', 'u4') or a dict of packing parameters as described
below or an iterable of such types, strings, or dicts.
This provides support for netCDF data packing as described in
https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/best_practices.html#bp_Packed-Data-Values
If this argument is a type (or type string), appropriate values of
scale_factor and add_offset will be automatically calculated based
on `cube.data` and possible masking. For more control, pass a dict with
one or more of the following keys: `dtype` (required), `scale_factor`
and `add_offset`. Note that automatic calculation of packing parameters
will trigger loading of lazy data; set them manually using a dict to
avoid this. The default is `None`, in which case the datatype is
determined from the cube and no packing will occur. If this argument is
a list it must have the same number of elements as `cube` if `cube` is
a `:class:`iris.cube.CubeList`, or one element, and each element of
this argument will be applied to each cube separately.
* fill_value (numeric or list):
The value to use for the `_FillValue` attribute on the netCDF variable.
If `packing` is specified the value of `fill_value` should be in the
domain of the packed data. If this argument is a list it must have the
same number of elements as `cube` if `cube` is a
`:class:`iris.cube.CubeList`, or a single element, and each element of
this argument will be applied to each cube separately.
Returns:
None.
.. note::
The `zlib`, `complevel`, `shuffle`, `fletcher32`, `contiguous`,
`chunksizes` and `endian` keywords are silently ignored for netCDF 3
files that do not use HDF5.
.. seealso::
NetCDF Context manager (:class:`~Saver`).
"""
from iris.cube import Cube, CubeList
if unlimited_dimensions is None:
unlimited_dimensions = []
if isinstance(cube, Cube):
cubes = CubeList()
cubes.append(cube)
else:
cubes = cube
if local_keys is None:
local_keys = set()
else:
local_keys = set(local_keys)
# Determine the attribute keys that are common across all cubes and
# thereby extend the collection of local_keys for attributes
# that should be attributes on data variables.
attributes = cubes[0].attributes
common_keys = set(attributes)
for cube in cubes[1:]:
keys = set(cube.attributes)
local_keys.update(keys.symmetric_difference(common_keys))
common_keys.intersection_update(keys)
different_value_keys = []
for key in common_keys:
if np.any(attributes[key] != cube.attributes[key]):
different_value_keys.append(key)
common_keys.difference_update(different_value_keys)
local_keys.update(different_value_keys)
def is_valid_packspec(p):
"""Only checks that the datatype is valid."""
if isinstance(p, dict):
if "dtype" in p:
return is_valid_packspec(p["dtype"])
else:
msg = "The argument to packing must contain the key 'dtype'."
raise ValueError(msg)
elif isinstance(p, str) or isinstance(p, type) or isinstance(p, str):
pdtype = np.dtype(p) # Does nothing if it's already a numpy dtype
if pdtype.kind != "i" and pdtype.kind != "u":
msg = "The packing datatype must be a numpy integer type."
raise ValueError(msg)
return True
elif p is None:
return True
else:
return False
if is_valid_packspec(packing):
packspecs = repeat(packing)
else:
# Assume iterable, make sure packing is the same length as cubes.
for cube, packspec in zip_longest(cubes, packing, fillvalue=-1):
if cube == -1 or packspec == -1:
msg = (
"If packing is a list, it must have the "
"same number of elements as the argument to"
"cube."
)
raise ValueError(msg)
if not is_valid_packspec(packspec):
msg = "Invalid packing argument: {}.".format(packspec)
raise ValueError(msg)
packspecs = packing
# Make fill-value(s) into an iterable over cubes.
if isinstance(fill_value, str):
# Strings are awkward -- handle separately.
fill_values = repeat(fill_value)
else:
try:
fill_values = tuple(fill_value)
except TypeError:
fill_values = repeat(fill_value)
else:
if len(fill_values) != len(cubes):
msg = (
"If fill_value is a list, it must have the "
"same number of elements as the cube argument."
)
raise ValueError(msg)
# Initialise Manager for saving
with Saver(filename, netcdf_format) as sman:
# Iterate through the cubelist.
for cube, packspec, fill_value in zip(cubes, packspecs, fill_values):
sman.write(
cube,
local_keys,
unlimited_dimensions,
zlib,
complevel,
shuffle,
fletcher32,
contiguous,
chunksizes,
endian,
least_significant_digit,
packing=packspec,
fill_value=fill_value,
)
if iris.config.netcdf.conventions_override:
# Set to the default if custom conventions are not available.
conventions = cube.attributes.get(
"Conventions", CF_CONVENTIONS_VERSION
)
else:
conventions = CF_CONVENTIONS_VERSION
# Perform a CF patch of the conventions attribute.
cf_profile_available = iris.site_configuration.get(
"cf_profile"
) not in [None, False]
if cf_profile_available:
conventions_patch = iris.site_configuration.get(
"cf_patch_conventions"
)
if conventions_patch is not None:
conventions = conventions_patch(conventions)
else:
msg = "cf_profile is available but no {} defined.".format(
"cf_patch_conventions"
)
warnings.warn(msg)
# Add conventions attribute.
sman.update_global_attributes(Conventions=conventions)