Provided by: python-cf_1.3.2+dfsg1-4_amd64 
NAME
cfdump - view CF fields
SYNOPSIS
cfdump [-1] [-c] [-h] [-i] [-l] [-n] [-s] [-u] [-x] [OPTIONS] INPUTS
DESCRIPTION
The cfdump tool generates text representations on standard output of the CF fields
contained in the INPUTS (which may include directories if the --recursive option is set).
Accepts CF-netCDF and CFA-netCDF files (or URLs if DAP access is enabled), Met Office (UK)
PP files and Met Office (UK) fields files as input. Multiple input files in a mixture of
formats may be given and normal UNIX file globbing rules apply.
By default the contents of each input file is aggregated (i.e. combined) into as few
multi-dimensional CF fields as possible. Unaggregatable fields in the input files may be
omitted from the output (see the -x option). Information on which fields are
unaggregatable, and why, may be displayed (see the --info option). All aggregation may be
turned off with the -n option, in which case all input fields are output without
modification.
See the AGGREGATION section for details on the aggregation process and unaggregatable
fields.
By default each input file is treated separately. In this case there is no inter-file
aggregation, but the contents of each file is aggregated independently of the others.
Alternatively, all of the input files may be treated collectively as a single CF dataset
(see the -1 option). In this case aggregation is attempted within and between the input
files.
In the displayed output, each component of a field is assigned one of the following roles
as defined by the CF data model:
Field
Axis
Cell method
Dimension coordinate
Auxiliary coordinate
Cell measure
Coordinate reference
A field and its components are identified, where appropriate, by their standard names if
available, or their long names. If neither is present then a netCDF variable name is used.
Long names and netCDF variable names are preceded by long_name: and ncvar: respectively.
Axis identities are inferred from the coordinates which span them.
Each data array of a field and its components is described by its dimensionality, units
and (depending on the extent of the output requested) its first and last values. For
longer and complete outputs, arrays containing coordinate bounds are given in the same way
and included as part of their coordinates' descriptions.
AGGREGATION
Aggregation of input fields into as few multi-dimensional CF fields as possible is carried
out according to the aggregation rules documented in CF ticket #78
(http://kitt.llnl.gov/trac/ticket/78). For each input field, the aggregation process
creates a structural signature which is essentially a subset of the metadata of the field,
including coordinate metadata and other domain information, but which contains no data
values. The structural signature accounts for the following standard CF properties:
add_offset, calendar, cell_methods, _FillValue, flag_masks, flag_meanings,
flag_values, missing_value, scale_factor, standard_error_multiplier, standard_name,
units, valid_max, valid_min, valid_range
Aggregation is then attempted on each group of fields with the same, well defined
structural signature, and will succeed where the coordinate data values imply a safe
combination into a single dataset.
Not all fields are aggregatable. Unaggregatable fields are those without a well defined
structural signature; or those with the same structural signature when at least two of
them 1) can't be unambiguously distinguished by coordinates or other domain information or
2) contain coordinate reference fields or ancillary variable fields which themselves can't
be unambiguously aggregated.
EXAMPLES
In these examples, a complete dataset has been split across two files (file1.nc and
file2.nc). These may be passed to cfdump which can return a description of the recombined,
aggregated field. The -1 option is necessary here so that the two input files are treated
as parts of the same dataset.
The -s option displays the short, one-line output, which gives the identity of the field
(air_temperature), the identities and sizes of its data array dimensions (time, latitude
and longitude with sizes 1200, 64 and 128 respectively) and the units of the field's data
array (K):
$ cfdump -1s file1.nc file2.nc
<CF Field: air_temperature(time(1200), latitude(64), longitude(128)) K>
The default summary gives the same information as the the one-line output, along with
short descriptions of the field's other components:
$ cfdump -1 file[12].nc
air_temperature field summary
-----------------------------
Data : air_temperature(time(1200), latitude(64), longitude(128)) K
Cell methods : time: mean (interval: 1.0 month)
Axes : time(12) = [ 450-11-16 00:00:00, ..., 550-10-16 12:00:00] noleap calendar
: latitude(64) = [-87.8638000488, ..., 87.8638000488] degrees_north
: longitude(128) = [0.0, ..., 357.1875] degrees_east
: height(1) = [2.0] m
This shows that the aggregated field has a cell method and four dimension coordinates, one
of which (height) is a coordinate for a size 1 dimension that is not a dimension of the
field's data array. The units and first and last values of the coordinates' data arrays
are given and relative time values are translated into strings.
The -l option displays the long output, which includes each component's properties, as
well as the first and last values of the field's data array:
$ cfdump -1l file[1-2].nc
======================
Field: air_temperature
======================
Axes
height(1)
latitude(64)
longitude(128)
time(12)
Data(time(12), latitude(64), longitude(128)) = [[[236.512756348, ..., 256.93371582]]] K
cell_methods = time: mean (interval: 1.0 month)
experiment_id = 'pre-industrial control experiment'
long_name = 'air_temperature'
missing_value = 1e+20
standard_name = 'air_temperature'
Dimension coordinate: time
Data(time(12)) = [ 450-11-16 00:00:00, ..., 550-10-16 12:00:00] noleap calendar
Bounds(time(12), 2) = [[ 450-11-01 00:00:00, ..., 550-11-01 00:00:00]] noleap calendar
axis = 'T'
standard_name = 'time'
Dimension coordinate: latitude
Data(latitude(64)) = [-87.8638000488, ..., 87.8638000488] degrees_north
Bounds(latitude(64), 2) = [[-90.0, ..., 90.0]] degrees_north
axis = 'Y'
standard_name = 'latitude'
Dimension coordinate: longitude
Data(longitude(128)) = [0.0, ..., 357.1875] degrees_east
Bounds(longitude(128), 2) = [[-1.40625, ..., 358.59375]] degrees_east
axis = 'X'
standard_name = 'longitude'
Dimension coordinate: height
Data(height(1)) = [2.0] m
axis = 'Z'
positive = 'up'
standard_name = 'height'
In this case, the complete output using the -c option would be the same as the long
output, since there are no fields contained in coordinate references nor ancillary
variables.
OPTIONS
-1, --one
Treat all input files collectively as a single CF dataset. In this case aggregation
is attempted within and between the input files.
--axis=property
Aggregation configuration: Create a new axis for each input field which has given
property. If an input field has the property then, prior to aggregation, a new axis
is created with an auxiliary coordinate whose data array is the property's value.
This allows for the possibility of aggregation along the new axis. The property
itself is deleted from that field. No axis is created for input fields which do not
have the specified property.
Multiple axes may be created by specifying more than one --axis option.
For example, if you wish to aggregate an ensemble of model experiments that are
distinguished by the source property, you can use --axis=source to create an
ensemble axis which has an auxiliary coordinate variable containing the source
property values.
-c, --complete
Display complete outputs. Fields are described without abbreviation with the
exception of data arrays, which are abbreviated to their first and last values.
Fields contained in transforms and ancillary variables are given as long outputs
(see the -l option).
--contiguous
Aggregation configuration: Requires that aggregated fields have adjacent dimension
coordinate cells which partially overlap or share common boundary values. Ignored
if the dimension coordinates do not have bounds.
--equal=property
Aggregation configuration: Require that an input field may only be aggregated with
other fields if they all have the given CF property (standard or non-standard) with
equal values. Ignored for any input field which does not have this property, or if
the property is already accounted for in the structural signature.
Supersedes the behaviour for the given property that may be implied by the
--exist_all option.
Multiple properties may be set by specifying more than one --equal option.
--equal_all
Aggregation configuration: Require that an input field may only be aggregated with
other fields that have the same set of CF properties (excluding those already
accounted for in the structural signature) with equal sets of values.
The behaviour for individual properties may be overridden by the --exist --ignore
options.
For example, to insist that a group of aggregated input fields must all have the
same CF properties (other than those accounted for in the structural signature)
with matching values, but allowing the long_name properties have unequal values,
you can use --equal_all --exist=long_name
--exist=property
Aggregation configuration: Require that an input field may only be aggregated with
other fields if they all have the given CF property (standard or non-standard), but
not requiring the values to be the same. Ignored for any input field which does not
have this property, or if the property is already accounted for in the structural
signature.
Supersedes the behaviour for the given property that may be implied by the
--equal_all option.
Multiple properties may be set by specifying more than one --exist option.
--exist_all
Aggregation configuration: Require that an input field may only be aggregated with
other fields that have the same set of CF properties (excluding those already
accounted for in the structural signature), but not requiring the values to be the
same.
The behaviour for individual properties may be overridden by the --equal --ignore
options.
For example, to insist that a group of aggregated input fields must all have the
same CF properties (other than those accounted for in the structural signature),
regardless of their values, but also insisting that the long_name properties have
equal values, you can use --exist_all --equal=long_name
--follow_symlinks
In combination with --recursive also search for files in directories which resolve
to symbolic links. Files specified by the INPUTS which are symbolic links are
always followed. Note that setting --recursive --follow_symlinks can lead to
infinite recursion if a directory which resolves to a symbolic link points to a
parent directory of itself.
-h, --help
Display this man page.
-i, --relaxed_identities
Aggregation configuration: In the absence of standard names, allow fields and their
components (such as coordinates) to be identified by their long_name CF properties
or else their netCDF file variable names.
--ignore=property
Aggregation configuration: An input field may be aggregated with other fields
regardless of whether or not they have the given CF property (standard or non-
standard) and regardless of its values. Ignored for any input field which does not
have this property, or if the property is already accounted for in the structural
signature.
This is the default behaviour in the absence of all the --exist --equal --exist_all
--equal_all options and supersedes the behaviour for the given property that may be
implied if any of these options are set.
Multiple properties may be set by specifying more than one --ignore option.
For example, to insist that a group of aggregated input fields must all have the
same CF properties (other than those accounted for in the structural signature)
with the same values, but with no restrictions on the existence or values of the
long_name property you can use --equal_all --ignore=long_name
--ignore_read_error
Ignore, without failing, any file which causes an error whilst being read, as would
be the case for an empty file, unknown file format, etc. By default, an error
occurs and the return code is non-zero.
--info=N
Print information about the aggregation process. If N is 0 then no information is
displayed. If N is 1 or more then display information on which fields are
unaggregatable, and why. If N is 2 or more then display the field structural
signatures and, when there is more than one field with the same structural
signature, their canonical first and last coordinate values. If N is 3 or more then
display the field complete aggregation metadata.
By default N is 1.
-l, --long
Display long outputs. Differs from the complete output (see the -c option) only in
that fields contained in transforms and ancillary variables are given as one-line
summaries (see the -s option) rather than as long outputs.
--ncvar_identities
Aggregation configuration: Force fields and their components (such as coordinates)
to be identified by their netCDF file variable names.
-n, --no_aggregation
Aggregation configuration: Do not aggregate fields. Displays the input fields as
they exist in the input files.
--no_overlap
Aggregation configuration: Requires that aggregated fields have adjacent dimension
coordinate cells which do not overlap (but they may share common boundary values).
Ignored if the dimension coordinates do not have bounds.
--promote=component
Promote field components to independent top-level fields. If component is ancillary
then ancillary data fields are promoted. If component is auxiliary then auxiliary
coordinate variables are promoted. If component is measure then cell meausure
variables are promoted. If component is reference then fields pointed to from
formula_terms attributes are promoted. If component is field then all component
fields are promoted.
Multiple conponent types may be promoted by specifying more than one --promote
option.
For example, promote ancillary data field and cell measure variables to
independent, top-level fields you can use --promote=ancillary --promote=measure
--respect_valid
Aggregation configuration: Take into account the CF properties valid_max, valid_min
and valid_range during aggregation. By default they are ignored for the purposes of
aggregation and deleted from any aggregated output CF fields.
-s, --short
Display short outputs. Fields are described by a short, one-line summaries.
--shared_nc_domain
Aggregation configuration: Match axes between a field and its contained ancillary
variable and coordinate reference fields via their netCDF dimension names and not
via their domains.
--squeeze
Remove size 1 axes from the displayed field data arrays. If a size one axis has any
one dimensional coordinates then these are converted to CF scalar coordinates.
--recursive
Allow directories to be specified by the INPUTS and recursively search the
directories for actual files to read. Set the --ignore_read_error option to bypass
any unreadable files and the --follow_symlinks option to allow directories to be
symbolic links.
-u, --relaxed_units
Aggregation configuration: Assume that fields or their components (such as
coordinates) with the same standard name (or other identifiers, see the -i option)
but missing units all have equivalent (but unspecified) units, so that aggregation
may occur. This is the default for Met Office (UK) PP files and Met Office (UK)
fields files, but not for other formats.
--unsqueeze
Include size 1 axes in the displayed field data arrays. If a size one axis has any
CF scalar coordinates then these are converted to one dimensional coordinates.
--um_version=version
For Met Office (UK) PP files and Met Office (UK) fields files only, the Unified
Model (UM) version to be used when decoding the header. Valid versions are, for
example, 4.2, 6.6.3 and 8.2. The default version is 4.5. In general, the given
version is ignored if it can be inferred from the header (which is usually the case
for files created by the UM at versions 5.3 and later). The exception to this is
when the given version has a third element (such as the 3 in 6.6.3), in which case
any version in the header is ignored. This option is ignored for input files which
are not Met Office (UK) PP files or Met Office (UK) fields files.
-x, --exclude
Aggregation configuration: Omit unaggregatable fields from the output. Ignored if
the -n option is set. See the AGGREGATION section for the definition of an
unaggregatable field.
SEE ALSO
cfa(1), ncdump(1)
LIBRARY
cf-python library version 1.3.1
BUGS
Reports of bugs are welcome at http://cfpython.bitbucket.org
LICENSE
Open Source Initiative MIT License
AUTHOR
David Hassell