cf.CellConnectivity

---

class cf.CellConnectivity(*args, **kwargs)

A cell connectivity construct of the CF data model.

A cell connectivity construct defines explicitly how cells arranged in two or three dimensions in real space but indexed by a single domain (discrete) axis are connected. Connectivity can only be provided when the domain axis construct also has a domain topology construct, and two cells can only be connected if they also have a topological relationship. For instance, the connectivity of two-dimensional face cells could be characterised by whether or not they have shared edges, where the edges are defined by connected nodes of the domain topology construct.

The cell connectivity construct consists of an array recording the connectivity, and properties to describe the data. There must be a property indicating the condition by which the connectivity is derived from the domain topology. The array spans the domain axis construct with the addition of a ragged dimension. For each cell, the first element along the ragged dimension contains the unique identity of the cell, and the following elements contain in arbitrary order the identities of all the other cells to which the cell is connected. Note that the connectivity array for point cells is, by definition, equivalent to the array of the domain topology construct.

When cell connectivity constructs are present they are considered to define the connectivity of the cells. Exactly the same connectivity information could be derived from the domain topology construct. Connectivity information inferred from inspection of any other constructs is not guaranteed to be the same.

In CF-netCDF a cell topology construct can only be provided by a UGRID mesh topology variable. The construct array is supplied either indirectly by any of the UGRID variables that are used to define a domain topology construct, or directly by the UGRID “face_face_connectivity” variable (for face cells). In the direct case, the integer indices contained in the UGRID variable may be used as the cell identities, although the CF data model attaches no significance to the values other than the fact that some values are the same as others.

Restricting the types of connectivity to those implied by the geospatial topology of the cells precludes connectivity derived from any other sources, but is consistent with UGRID encoding within CF-netCDF.

See CF Appendix I “The CF Data Model”.

NetCDF interface

The netCDF variable name may be accessed with the nc_set_variable, nc_get_variable, nc_del_variable, and nc_has_variable methods.

The netCDF variable group structure may be accessed with the nc_set_variable, nc_get_variable, nc_variable_groups, nc_clear_variable_groups, and nc_set_variable_groups methods.

Added in version 3.16.0.

Initialisation

Parameters:

connectivity: str, optional

The connectivity type describes a characteristic of inter-cell connectivity defined by the domain topology construct. It may take any value, but the following values are standardised: 'node'``(edge or face cells connected by one or more shared nodes) and ``'edge' (face cells connected by one or more shared edges).

properties: dict, optional

Set descriptive properties. The dictionary keys are property names, with corresponding values.

Properties may also be set after initialisation with the set_properties and set_property methods.

Parameter example:

properties={'long_name': 'face-face connectivity'}

data: data_like, optional

Set the data.

A data_like object is any object that can be converted to a Data object, i.e. numpy array_like objects, Data objects, and cf instances that contain Data objects.

The data also may be set after initialisation with the set_data method.

source: optional

Convert source, which can be any type of object, to a CellConnectivity instance.

All other parameters, apart from copy, are ignored and their values are instead inferred from source by assuming that it has the CellConnectivity API. Any parameters that can not be retrieved from source in this way are assumed to have their default value.

Note that if x is also a CellConnectivity instance then cf.CellConnectivity(source=x) is equivalent to x.copy().

copy: bool, optional

If True (the default) then deep copy the input parameters prior to initialisation. By default the parameters are not deep copied.

Inspection

Methods

dump	A full description of the cell connectivity construct.
identity	Return the canonical identity.
identities	Return all possible identities.
inspect	Inspect the object for debugging.

Attributes

construct_type

Return a description of the construct type.

Topology

Methods

del_connectivity	Remove the connectivity.
get_connectivity	Return the connectivity type.
has_connectivity	Whether the connectivity type has been set.
set_connectivity	Set the connectivity type.
normalise	Normalise the data values.

Attributes

connectivity

The connectivity type.

Selection

Methods

match_by_identity	Whether or not the construct identity satisfies conditions.
match_by_naxes	Whether or not the data has a given dimensionality.
match_by_ncvar	Whether or not the netCDF variable name satisfies conditions.
match_by_property	Whether or not properties satisfy conditions.
match_by_units	Whether or not the construct has given units.

Properties

Methods

del_property	Remove a property.
get_property	Get a CF property.
has_property	Whether a property has been set.
set_property	Set a property.
properties	Return all properties.
clear_properties	Remove all properties.
del_properties	Remove properties.
set_properties	Set properties.

Attributes

add_offset	The add_offset CF property.
calendar	The calendar CF property.
comment	The comment CF property.
_FillValue	The _FillValue CF property.
history	The history CF property.
leap_month	The leap_month CF property.
leap_year	The leap_year CF property.
long_name	The long_name CF property.
missing_value	The missing_value CF property.
month_lengths	The month_lengths CF property.
scale_factor	The scale_factor CF property.
standard_name	The standard_name CF property.
units	The units CF property.
valid_max	The valid_max CF property.
valid_min	The valid_min CF property.
valid_range	The valid_range CF property.

Units

Methods

to_units	Change the data array units.
override_units	Override the units.
override_calendar	Override the calendar of date-time units.

Attributes

Units

The cf.Units object containing the units of the data array.

Data

Attributes

array	A numpy array deep copy of the data.
Data	Deprecated at version 3.0.0, use data attribute or get_data method instead.
data	The Data object containing the data array.
datetime_array	An independent numpy array of date-time objects.
datum	Return an element of the data array as a standard Python scalar.
dtype	The numpy data type of the data array.
isscalar	True if the data array is scalar.
ndim	The number of data dimensions.
shape	A tuple of the data array's dimension sizes.
size	The number elements in the data.
varray	A numpy array view of the data.

Methods

to_dask_array	Convert the data to a dask array.
__getitem__	Return a subspace defined by indices.
del_data	Remove the data.
get_data	Return the data.
has_data	Whether or not the construct has data.
set_data	Set the data.

Rearranging elements

flatten	Flatten axes of the data.
flip	Flip (reverse the direction of) data dimensions.
insert_dimension	Expand the shape of the data array.
roll	Roll the data along one or more axes.
squeeze	Remove size one axes from the data array.
swapaxes	Interchange two axes of an array.
transpose	Permute the axes of the data array.

Expanding the data

halo	Expand the data by adding a halo.
pad_missing	Pad an axis with missing data.

Data array mask

apply_masking	Apply masking as defined by the CF conventions.
count	Count the non-masked elements of the data.
count_masked	Count the masked elements of the data.
fill_value	Return the data array missing data value.
filled	Replace masked elements with a fill value.
masked_invalid	Mask the array where invalid values occur (NaN or inf).

binary_mask	A binary (0 and 1) missing data mask of the data array.
hardmask	Whether the mask is hard (True) or soft (False).
mask	The mask of the data array.

Changing data values

__setitem__	Called to implement assignment to x[indices]
masked_invalid	Mask the array where invalid values occur (NaN or inf).
subspace	Return a new variable whose data is subspaced.
where	Set data array elements depending on a condition.

Miscellaneous

rechunk	Change the chunk structure of the data.
close	Close all files referenced by the construct.
convert_reference_time	Convert reference time data values to have new units.
cyclic	Get or set the cyclicity of an axis.
period	Return or set the period of the data.
iscyclic	Whether or not a given axis is cyclic.
isperiodic	True if a given axis is periodic.
get_original_filenames	The names of files containing the original data and metadata.
has_bounds	Whether or not there are cell bounds.
persist	Persist data into memory.

Quantization

Methods

get_quantization	Get quantization metadata.
get_quantize_on_write	Get a quantize-on-write instruction.

Miscellaneous

Methods

concatenate	Join a together sequence of CellConnectivity.
copy	Return a deep copy.
creation_commands	Returns the commands to create the construct.
equals	Whether two instances are the same.
to_memory	Bring data on disk into memory.
uncompress	Uncompress the construct.

Attributes

T	True if and only if the data are coordinates for a CF 'T' axis.
X	Always False.
Y	Always False.
Z	Always False.
id	An identity for the CellConnectivity object.

Mathematical operations

Methods

Trigonometrical and hyperbolic functions

arccos	Take the trigonometric inverse cosine of the data element- wise.
arccosh	Take the inverse hyperbolic cosine of the data element-wise.
arcsin	Take the trigonometric inverse sine of the data element-wise.
arcsinh	Take the inverse hyperbolic sine of the data element-wise.
arctan	Take the trigonometric inverse tangent of the data element- wise.
arctanh	Take the inverse hyperbolic tangent of the data element-wise.
cos	Take the trigonometric cosine of the data element-wise.
cosh	Take the hyperbolic cosine of the data element-wise.
sin	Take the trigonometric sine of the data element-wise.
sinh	Take the hyperbolic sine of the data element-wise.
tan	Take the trigonometric tangent of the data element-wise.
tanh	Take the hyperbolic tangent of the data array.

Rounding and truncation

ceil	The ceiling of the data, element-wise.
clip	Limit the values in the data.
floor	Floor the data array, element-wise.
rint	Round the data to the nearest integer, element-wise.
round	Round the data to the given number of decimals.
trunc	Truncate the data, element-wise.

Statistical collapses

max	Alias for maximum.
mean	The unweighted mean the data array.
mid_range	The unweighted average of the maximum and minimum of the data array.
min	Alias for minimum.
range	The absolute difference between the maximum and minimum of the data array.
sample_size	The number of non-missing data elements in the data array.
sum	The sum of the data array.
sd	Alias for standard_deviation
var	Alias for variance
standard_deviation	The unweighted sample standard deviation of the data array.
variance	The unweighted sample variance of the data array.
maximum	The maximum of the data array.
minimum	The minimum of the data array.

Exponential and logarithmic functions

exp	The exponential of the data, element-wise.
log	The logarithm of the data array.

Date-time operations

Attributes

day	The day of each date-time data array element.
datetime_array	An independent numpy array of date-time objects.
hour	The hour of each date-time data array element.
minute	The minute of each date-time data array element.
month	The month of each date-time data array element.
reference_datetime	The reference date-time of units of elapsed time.
second	The second of each date-time data array element.
year	The year of each date-time data array element.

Logic functions

Truth value testing

all	Test whether all data elements evaluate to True.
any	Test whether any data elements evaluate to True.

Comparison

allclose	Test whether all data are element-wise equal to other, broadcastable data.
equals	Whether two instances are the same.
equivalent	True if two constructs are equal, False otherwise.

Set operations

unique

The unique elements of the data.

NetCDF

Methods

nc_del_variable	Remove the netCDF variable name.
nc_get_variable	Return the netCDF variable name.
nc_has_variable	Whether the netCDF variable name has been set.
nc_set_variable	Set the netCDF variable name.
nc_clear_dataset_chunksizes	Clear the dataset chunking strategy for the data.
nc_dataset_chunksizes	Get the dataset chunking strategy for the data.
nc_set_dataset_chunksizes	Set the dataset chunking strategy.

Aggregation

Methods

file_directories	The directories of files containing parts of the data.
replace_directory	Replace a file directory in-place.

NetCDF

Methods

nc_del_variable	Remove the netCDF variable name.
nc_get_variable	Return the netCDF variable name.
nc_has_variable	Whether the netCDF variable name has been set.
nc_set_variable	Set the netCDF variable name.

Groups

Methods

nc_variable_groups	Return the netCDF variable group hierarchy.
nc_clear_variable_groups	Remove the netCDF variable group hierarchy.
nc_set_variable_groups	Set the netCDF variable group hierarchy.

Dataset chunks

Methods

nc_dataset_chunksizes	Get the dataset chunking strategy for the data.
nc_set_dataset_chunksizes	Set the dataset chunking strategy.
nc_clear_dataset_chunksizes	Clear the dataset chunking strategy for the data.

Aliases

Methods

match

Alias for match_by_identity.

Attributes

dtarray

Alias for datetime_array.

Special

Methods

__deepcopy__	Called by the copy.deepcopy function.
__getitem__	Return a subspace defined by indices.
__repr__	Called by the repr built-in function.
__str__	Called by the str built-in function.

Docstring substitutions

Methods

_docstring_special_substitutions	Return the special docstring substitutions.
_docstring_substitutions	Returns the substitutions that apply to methods of the class.
_docstring_package_depth	Returns the class {{package}} substitutions package depth.
_docstring_method_exclusions	Returns method names excluded in the class substitutions.

Deprecated

Methods

asdatetime	Deprecated at version 3.0.0.
asreftime	Deprecated at version 3.0.0.
attributes	Deprecated at version 3.0.0.
chunk	Partition the data array.
delprop	Deprecated at version 3.0.0, use method del_property instead.
dtvarray	Deprecated at version 3.0.0.
expand_dims	Deprecated at version 3.0.0, use insert_dimension method instead.
get_filenames	Return the name of the file or files containing the data.
getprop	Deprecated at version 3.0.0, use method get_property instead.
hasbounds	Deprecated at version 3.0.0, use has_bounds method instead.
hasdata	Deprecated at version 3.0.0, use has_data method instead.
hasprop	Deprecated at version 3.0.0, use method has_property instead.
insert_data	Deprecated at version 3.0.0, use set_data method instead.
isauxiliary	Deprecated at version 3.7.0, use construct_type attribute instead.
isdimension	Deprecated at version 3.7.0, use construct_type attribute instead.
isdomainancillary	Deprecated at version 3.7.0, use construct_type attribute instead.
isfieldancillary	Deprecated at version 3.7.0, use construct_type attribute instead.
ismeasure	Deprecated at version 3.7.0, use construct_type attribute instead.
mask_invalid	Mask the array where invalid values occur.
name	Deprecated at version 3.0.0, use method 'identity' instead.
remove_data	Deprecated at version 3.0.0, use method del_data instead.
select	Deprecated at version 3.0.0.
setprop	Deprecated at version 3.0.0, use method set_property instead.
unsafe_array	Deprecated at version 3.0.0, use array attribute instead.
nc_clear_hdf5_chunksizes	Clear the HDF5 chunking strategy for the data.
nc_hdf5_chunksizes	Get the HDF5 chunking strategy for the data.
nc_set_hdf5_chunksizes	Set the HDF5 chunking strategy.