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<article id="content">
<header>
<h1 class="title">Package <code>netCDF4</code></h1>
</header>
<section id="section-intro">
<h2 id="version-172">Version 1.7.2</h2>
<h1 id="introduction">Introduction</h1>
<p>netcdf4-python is a Python interface to the netCDF C library.</p>
<p><a href="http://www.unidata.ucar.edu/software/netcdf/">netCDF</a> version 4 has many features
not found in earlier versions of the library and is implemented on top of
<a href="http://www.hdfgroup.org/HDF5">HDF5</a>. This module can read and write
files in both the new netCDF 4 and the old netCDF 3 format, and can create
files that are readable by HDF5 clients. The API modelled after
<a href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific.IO.NetCDF</a>,
and should be familiar to users of that module.</p>
<p>Most new features of netCDF 4 are implemented, such as multiple
unlimited dimensions, groups and data compression.
All the new
numeric data types (such as 64 bit and unsigned integer types) are
implemented. Compound (struct), variable length (vlen) and
enumerated (enum) data types are supported, but not the opaque data type.
Mixtures of compound, vlen and enum data types (such as
compound types containing enums, or vlens containing compound
types) are not supported.</p>
<h2 id="quick-install">Quick Install</h2>
<ul>
<li>the easiest way to get going is to install via <code>pip install <a title="netCDF4" href="#netCDF4">netCDF4</a></code>.
(or if you use the <a href="http://conda.io">conda</a> package manager <code>conda install -c conda-forge netCDF4</code>).</li>
</ul>
<h2 id="developer-install">Developer Install</h2>
<ul>
<li>Clone the <a href="http://github.com/Unidata/netcdf4-python">github repository</a>. Make
sure you either clone recursively, or run <code>git submodule update --init</code> to
ensure all the submodules are also checked out.</li>
<li>Make sure the dependencies are satisfied (Python 3.8 or later,
<a href="http://numpy.scipy.org">numpy</a>,
<a href="http://cython.org">Cython</a>,
<a href="https://github.com/Unidata/cftime">cftime</a>,
<a href="https://pypi.python.org/pypi/setuptools">setuptools</a>,
the <a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5 C library</a>,
and the <a href="https://www.unidata.ucar.edu/software/netcdf/">netCDF C library</a>).
For MPI parallel IO support, an MPI-enabled versions of the netcdf library
is required, as is <a href="http://mpi4py.scipy.org">mpi4py</a>.
Parallel IO further depends on the existence of MPI-enabled HDF5 or the
<a href="https://parallel-netcdf.github.io/">PnetCDF</a> library.</li>
<li>By default, the utility <code>nc-config</code> (installed with netcdf-c)
will be run used to determine where all the dependencies live.</li>
<li>If <code>nc-config</code> is not in your default <code>PATH</code>, you can set the <code>NETCDF4_DIR</code>
environment variable and <code>setup.py</code> will look in <code>$NETCDF4_DIR/bin</code>.
You can also use the file <code>setup.cfg</code> to set the path to <code>nc-config</code>, or
enter the paths to the libraries and include files manually. Just
edit the <code>setup.cfg</code> file
in a text editor and follow the instructions in the comments.
To disable the use of <code>nc-config</code>, set the env var <code>USE_NCCONFIG</code> to 0.
To disable the use of <code>setup.cfg</code>, set <code>USE_SETUPCFG</code> to 0.
As a last resort, the library and include paths can be set via environment variables.
If you go this route, set <code>USE_NCCONFIG</code> and <code>USE_SETUPCFG</code> to 0, and specify
<code>NETCDF4_LIBDIR</code>, <code>NETCDF4_INCDIR</code>, <code>HDF5_LIBDIR</code> and <code>HDF5_INCDIR</code>.
If the dependencies are not found
in any of the paths specified by environment variables, then standard locations
(such as <code>/usr</code> and <code>/usr/local</code>) are searched.</li>
<li>if the env var <code>NETCDF_PLUGIN_DIR</code> is set to point to the location of the netcdf-c compression
plugins built by netcdf >= 4.9.0, they will be installed inside the package.
In this
case <code>HDF5_PLUGIN_PATH</code> will be set to the package installation path on import,
so the extra compression algorithms available in netcdf-c >= 4.9.0 will automatically
be available.
Otherwise, the user will have to set <code>HDF5_PLUGIN_PATH</code> explicitly
to have access to the extra compression plugins.</li>
<li>run <code>pip install -v .</code> (as root if necessary)</li>
<li>run the tests in the 'test' directory by running <code>python run_all.py</code>.</li>
</ul>
<h1 id="tutorial">Tutorial</h1>
<ul>
<li><a href="#creatingopeningclosing-a-netcdf-file">Creating/Opening/Closing a netCDF file</a></li>
<li><a href="#groups-in-a-netcdf-file">Groups in a netCDF file</a></li>
<li><a href="#dimensions-in-a-netcdf-file">Dimensions in a netCDF file</a></li>
<li><a href="#variables-in-a-netcdf-file">Variables in a netCDF file</a></li>
<li><a href="#attributes-in-a-netcdf-file">Attributes in a netCDF file</a></li>
<li><a href="#dealing-with-time-coordinates">Dealing with time coordinates</a></li>
<li><a href="#writing-data-to-and-retrieving-data-from-a-netcdf-variable">Writing data to and retrieving data from a netCDF variable</a></li>
<li><a href="#reading-data-from-a-multi-file-netcdf-dataset">Reading data from a multi-file netCDF dataset</a></li>
<li><a href="#efficient-compression-of-netcdf-variables">Efficient compression of netCDF variables</a></li>
<li><a href="#beyond-homogeneous-arrays-of-a-fixed-type-compound-data-types">Beyond homogeneous arrays of a fixed type - compound data types</a></li>
<li><a href="#variable-length-vlen-data-types">Variable-length (vlen) data types</a></li>
<li><a href="#enum-data-type">Enum data type</a></li>
<li><a href="#parallel-io">Parallel IO</a></li>
<li><a href="#dealing-with-strings">Dealing with strings</a></li>
<li><a href="#in-memory-diskless-datasets">In-memory (diskless) Datasets</a></li>
</ul>
<p>All of the code in this tutorial is available in <code>examples/tutorial.py</code>, except
the parallel IO example, which is in <code>examples/mpi_example.py</code>.
Unit tests are in the <code>test</code> directory.</p>
<h2 id="creatingopeningclosing-a-netcdf-file">Creating/Opening/Closing a netCDF file</h2>
<p>To create a netCDF file from python, you simply call the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>
constructor. This is also the method used to open an existing netCDF
file.
If the file is open for write access (<code>mode='w', 'r+'</code> or <code>'a'</code>), you may
write any type of data including new dimensions, groups, variables and
attributes.
netCDF files come in five flavors (<code>NETCDF3_CLASSIC</code>,
<code>NETCDF3_64BIT_OFFSET</code>, <code>NETCDF3_64BIT_DATA</code>, <code>NETCDF4_CLASSIC</code>, and <code>NETCDF4</code>).
<code>NETCDF3_CLASSIC</code> was the original netcdf binary format, and was limited
to file sizes less than 2 Gb. <code>NETCDF3_64BIT_OFFSET</code> was introduced
in version 3.6.0 of the library, and extended the original binary format
to allow for file sizes greater than 2 Gb.
<code>NETCDF3_64BIT_DATA</code> is a new format that requires version 4.4.0 of
the C library - it extends the <code>NETCDF3_64BIT_OFFSET</code> binary format to
allow for unsigned/64 bit integer data types and 64-bit dimension sizes.
<code>NETCDF3_64BIT</code> is an alias for <code>NETCDF3_64BIT_OFFSET</code>.
<code>NETCDF4_CLASSIC</code> files use the version 4 disk format (HDF5), but omits features
not found in the version 3 API. They can be read by netCDF 3 clients
only if they have been relinked against the netCDF 4 library. They can
also be read by HDF5 clients. <code>NETCDF4</code> files use the version 4 disk
format (HDF5) and use the new features of the version 4 API.
The
netCDF4 module can read and write files in any of these formats. When
creating a new file, the format may be specified using the <code>format</code>
keyword in the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> constructor.
The default format is
<code>NETCDF4</code>. To see how a given file is formatted, you can examine the
<code>data_model</code> attribute.
Closing the netCDF file is
accomplished via the <code><a title="netCDF4.Dataset.close" href="#netCDF4.Dataset.close">Dataset.close()</a></code> method of the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>
instance.</p>
<p>Here's an example:</p>
<pre><code class="language-python">>>> from netCDF4 import Dataset
>>> rootgrp = Dataset("test.nc", "w", format="NETCDF4")
>>> print(rootgrp.data_model)
NETCDF4
>>> rootgrp.close()
</code></pre>
<p>Remote <a href="http://opendap.org">OPeNDAP</a>-hosted datasets can be accessed for
reading over http if a URL is provided to the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> constructor instead of a
filename.
However, this requires that the netCDF library be built with
OPenDAP support, via the <code>--enable-dap</code> configure option (added in
version 4.0.1).</p>
<h2 id="groups-in-a-netcdf-file">Groups in a netCDF file</h2>
<p>netCDF version 4 added support for organizing data in hierarchical
groups, which are analogous to directories in a filesystem. Groups serve
as containers for variables, dimensions and attributes, as well as other
groups.
A <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> creates a special group, called
the 'root group', which is similar to the root directory in a unix
filesystem.
To create <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instances, use the
<code><a title="netCDF4.Dataset.createGroup" href="#netCDF4.Dataset.createGroup">Dataset.createGroup()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code>
instance. <code><a title="netCDF4.Dataset.createGroup" href="#netCDF4.Dataset.createGroup">Dataset.createGroup()</a></code> takes a single argument, a
python string containing the name of the new group. The new <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code>
instances contained within the root group can be accessed by name using
the <code>groups</code> dictionary attribute of the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> instance.
Only
<code>NETCDF4</code> formatted files support Groups, if you try to create a Group
in a netCDF 3 file you will get an error message.</p>
<pre><code class="language-python">>>> rootgrp = Dataset("test.nc", "a")
>>> fcstgrp = rootgrp.createGroup("forecasts")
>>> analgrp = rootgrp.createGroup("analyses")
>>> print(rootgrp.groups)
{'forecasts': <class 'netCDF4._netCDF4.Group'>
group /forecasts:
dimensions(sizes):
variables(dimensions):
groups: , 'analyses': <class 'netCDF4._netCDF4.Group'>
group /analyses:
dimensions(sizes):
variables(dimensions):
groups: }
>>>
</code></pre>
<p>Groups can exist within groups in a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>, just as directories
exist within directories in a unix filesystem. Each <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance
has a <code>groups</code> attribute dictionary containing all of the group
instances contained within that group. Each <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance also has a
<code>path</code> attribute that contains a simulated unix directory path to
that group.
To simplify the creation of nested groups, you can
use a unix-like path as an argument to <code><a title="netCDF4.Dataset.createGroup" href="#netCDF4.Dataset.createGroup">Dataset.createGroup()</a></code>.</p>
<pre><code class="language-python">>>> fcstgrp1 = rootgrp.createGroup("/forecasts/model1")
>>> fcstgrp2 = rootgrp.createGroup("/forecasts/model2")
</code></pre>
<p>If any of the intermediate elements of the path do not exist, they are created,
just as with the unix command <code>'mkdir -p'</code>. If you try to create a group
that already exists, no error will be raised, and the existing group will be
returned.</p>
<p>Here's an example that shows how to navigate all the groups in a
<code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>. The function <code>walktree</code> is a Python generator that is used
to walk the directory tree. Note that printing the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code>
object yields summary information about it's contents.</p>
<pre><code class="language-python">>>> def walktree(top):
... yield top.groups.values()
... for value in top.groups.values():
... yield from walktree(value)
>>> print(rootgrp)
<class 'netCDF4._netCDF4.Dataset'>
root group (NETCDF4 data model, file format HDF5):
dimensions(sizes):
variables(dimensions):
groups: forecasts, analyses
>>> for children in walktree(rootgrp):
... for child in children:
... print(child)
<class 'netCDF4._netCDF4.Group'>
group /forecasts:
dimensions(sizes):
variables(dimensions):
groups: model1, model2
<class 'netCDF4._netCDF4.Group'>
group /analyses:
dimensions(sizes):
variables(dimensions):
groups:
<class 'netCDF4._netCDF4.Group'>
group /forecasts/model1:
dimensions(sizes):
variables(dimensions):
groups:
<class 'netCDF4._netCDF4.Group'>
group /forecasts/model2:
dimensions(sizes):
variables(dimensions):
groups:
</code></pre>
<h2 id="dimensions-in-a-netcdf-file">Dimensions in a netCDF file</h2>
<p>netCDF defines the sizes of all variables in terms of dimensions, so
before any variables can be created the dimensions they use must be
created first. A special case, not often used in practice, is that of a
scalar variable, which has no dimensions. A dimension is created using
the <code><a title="netCDF4.Dataset.createDimension" href="#netCDF4.Dataset.createDimension">Dataset.createDimension()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>
or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance. A Python string is used to set the name of the
dimension, and an integer value is used to set the size. To create an
unlimited dimension (a dimension that can be appended to), the size
value is set to <code>None</code> or 0. In this example, there both the <code>time</code> and
<code>level</code> dimensions are unlimited.
Having more than one unlimited
dimension is a new netCDF 4 feature, in netCDF 3 files there may be only
one, and it must be the first (leftmost) dimension of the variable.</p>
<pre><code class="language-python">>>> level = rootgrp.createDimension("level", None)
>>> time = rootgrp.createDimension("time", None)
>>> lat = rootgrp.createDimension("lat", 73)
>>> lon = rootgrp.createDimension("lon", 144)
</code></pre>
<p>All of the <code><a title="netCDF4.Dimension" href="#netCDF4.Dimension">Dimension</a></code> instances are stored in a python dictionary.</p>
<pre><code class="language-python">>>> print(rootgrp.dimensions)
{'level': <class 'netCDF4._netCDF4.Dimension'> (unlimited): name = 'level', size = 0, 'time': <class 'netCDF4._netCDF4.Dimension'> (unlimited): name = 'time', size = 0, 'lat': <class 'netCDF4._netCDF4.Dimension'>: name = 'lat', size = 73, 'lon': <class 'netCDF4._netCDF4.Dimension'>: name = 'lon', size = 144}
</code></pre>
<p>Using the python <code>len</code> function with a <code><a title="netCDF4.Dimension" href="#netCDF4.Dimension">Dimension</a></code> instance returns
current size of that dimension.
<code><a title="netCDF4.Dimension.isunlimited" href="#netCDF4.Dimension.isunlimited">Dimension.isunlimited()</a></code> method of a <code><a title="netCDF4.Dimension" href="#netCDF4.Dimension">Dimension</a></code> instance
be used to determine if the dimensions is unlimited, or appendable.</p>
<pre><code class="language-python">>>> print(len(lon))
144
>>> print(lon.isunlimited())
False
>>> print(time.isunlimited())
True
</code></pre>
<p>Printing the <code><a title="netCDF4.Dimension" href="#netCDF4.Dimension">Dimension</a></code> object
provides useful summary info, including the name and length of the dimension,
and whether it is unlimited.</p>
<pre><code class="language-python">>>> for dimobj in rootgrp.dimensions.values():
... print(dimobj)
<class 'netCDF4._netCDF4.Dimension'> (unlimited): name = 'level', size = 0
<class 'netCDF4._netCDF4.Dimension'> (unlimited): name = 'time', size = 0
<class 'netCDF4._netCDF4.Dimension'>: name = 'lat', size = 73
<class 'netCDF4._netCDF4.Dimension'>: name = 'lon', size = 144
</code></pre>
<p><code><a title="netCDF4.Dimension" href="#netCDF4.Dimension">Dimension</a></code> names can be changed using the
<code><a title="netCDF4.Dataset.renameDimension" href="#netCDF4.Dataset.renameDimension">Dataset.renameDimension()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or
<code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance.</p>
<h2 id="variables-in-a-netcdf-file">Variables in a netCDF file</h2>
<p>netCDF variables behave much like python multidimensional array objects
supplied by the <a href="http://numpy.scipy.org">numpy module</a>. However,
unlike numpy arrays, netCDF4 variables can be appended to along one or
more 'unlimited' dimensions. To create a netCDF variable, use the
<code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or
<code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance. The <code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code>j method
has two mandatory arguments, the variable name (a Python string), and
the variable datatype. The variable's dimensions are given by a tuple
containing the dimension names (defined previously with
<code><a title="netCDF4.Dataset.createDimension" href="#netCDF4.Dataset.createDimension">Dataset.createDimension()</a></code>). To create a scalar
variable, simply leave out the dimensions keyword. The variable
primitive datatypes correspond to the dtype attribute of a numpy array.
You can specify the datatype as a numpy dtype object, or anything that
can be converted to a numpy dtype object.
Valid datatype specifiers
include: <code>'f4'</code> (32-bit floating point), <code>'f8'</code> (64-bit floating
point), <code>'i4'</code> (32-bit signed integer), <code>'i2'</code> (16-bit signed
integer), <code>'i8'</code> (64-bit signed integer), <code>'i1'</code> (8-bit signed
integer), <code>'u1'</code> (8-bit unsigned integer), <code>'u2'</code> (16-bit unsigned
integer), <code>'u4'</code> (32-bit unsigned integer), <code>'u8'</code> (64-bit unsigned
integer), or <code>'S1'</code> (single-character string).
The old Numeric
single-character typecodes (<code>'f'</code>,<code>'d'</code>,<code>'h'</code>,
<code>'s'</code>,<code>'b'</code>,<code>'B'</code>,<code>'c'</code>,<code>'i'</code>,<code>'l'</code>), corresponding to
(<code>'f4'</code>,<code>'f8'</code>,<code>'i2'</code>,<code>'i2'</code>,<code>'i1'</code>,<code>'i1'</code>,<code>'S1'</code>,<code>'i4'</code>,<code>'i4'</code>),
will also work. The unsigned integer types and the 64-bit integer type
can only be used if the file format is <code>NETCDF4</code>.</p>
<p>The dimensions themselves are usually also defined as variables, called
coordinate variables. The <code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code>
method returns an instance of the <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> class whose methods can be
used later to access and set variable data and attributes.</p>
<pre><code class="language-python">>>> times = rootgrp.createVariable("time","f8",("time",))
>>> levels = rootgrp.createVariable("level","i4",("level",))
>>> latitudes = rootgrp.createVariable("lat","f4",("lat",))
>>> longitudes = rootgrp.createVariable("lon","f4",("lon",))
>>> # two dimensions unlimited
>>> temp = rootgrp.createVariable("temp","f4",("time","level","lat","lon",))
>>> temp.units = "K"
</code></pre>
<p>To get summary info on a <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> instance in an interactive session,
just print it.</p>
<pre><code class="language-python">>>> print(temp)
<class 'netCDF4._netCDF4.Variable'>
float32 temp(time, level, lat, lon)
units: K
unlimited dimensions: time, level
current shape = (0, 0, 73, 144)
filling on, default _FillValue of 9.969209968386869e+36 used
</code></pre>
<p>You can use a path to create a Variable inside a hierarchy of groups.</p>
<pre><code class="language-python">>>> ftemp = rootgrp.createVariable("/forecasts/model1/temp","f4",("time","level","lat","lon",))
</code></pre>
<p>If the intermediate groups do not yet exist, they will be created.</p>
<p>You can also query a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance directly to obtain <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> or
<code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> instances using paths.</p>
<pre><code class="language-python">>>> print(rootgrp["/forecasts/model1"]) # a Group instance
<class 'netCDF4._netCDF4.Group'>
group /forecasts/model1:
dimensions(sizes):
variables(dimensions): float32 temp(time,level,lat,lon)
groups:
>>> print(rootgrp["/forecasts/model1/temp"]) # a Variable instance
<class 'netCDF4._netCDF4.Variable'>
float32 temp(time, level, lat, lon)
path = /forecasts/model1
unlimited dimensions: time, level
current shape = (0, 0, 73, 144)
filling on, default _FillValue of 9.969209968386869e+36 used
</code></pre>
<p>All of the variables in the <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> are stored in a
Python dictionary, in the same way as the dimensions:</p>
<pre><code class="language-python">>>> print(rootgrp.variables)
{'time': <class 'netCDF4._netCDF4.Variable'>
float64 time(time)
unlimited dimensions: time
current shape = (0,)
filling on, default _FillValue of 9.969209968386869e+36 used, 'level': <class 'netCDF4._netCDF4.Variable'>
int32 level(level)
unlimited dimensions: level
current shape = (0,)
filling on, default _FillValue of -2147483647 used, 'lat': <class 'netCDF4._netCDF4.Variable'>
float32 lat(lat)
unlimited dimensions:
current shape = (73,)
filling on, default _FillValue of 9.969209968386869e+36 used, 'lon': <class 'netCDF4._netCDF4.Variable'>
float32 lon(lon)
unlimited dimensions:
current shape = (144,)
filling on, default _FillValue of 9.969209968386869e+36 used, 'temp': <class 'netCDF4._netCDF4.Variable'>
float32 temp(time, level, lat, lon)
units: K
unlimited dimensions: time, level
current shape = (0, 0, 73, 144)
filling on, default _FillValue of 9.969209968386869e+36 used}
</code></pre>
<p><code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> names can be changed using the
<code><a title="netCDF4.Dataset.renameVariable" href="#netCDF4.Dataset.renameVariable">Dataset.renameVariable()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>
instance.</p>
<p>Variables can be sliced similar to numpy arrays, but there are some differences.
See
<a href="#writing-data-to-and-retrieving-data-from-a-netcdf-variable">Writing data to and retrieving data from a netCDF variable</a> for more details.</p>
<h2 id="attributes-in-a-netcdf-file">Attributes in a netCDF file</h2>
<p>There are two types of attributes in a netCDF file, global and variable.
Global attributes provide information about a group, or the entire
dataset, as a whole. <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> attributes provide information about
one of the variables in a group. Global attributes are set by assigning
values to <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance variables. <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code>
attributes are set by assigning values to <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> instances
variables. Attributes can be strings, numbers or sequences. Returning to
our example,</p>
<pre><code class="language-python">>>> import time
>>> rootgrp.description = "bogus example script"
>>> rootgrp.history = "Created " + time.ctime(time.time())
>>> rootgrp.source = "netCDF4 python module tutorial"
>>> latitudes.units = "degrees north"
>>> longitudes.units = "degrees east"
>>> levels.units = "hPa"
>>> temp.units = "K"
>>> times.units = "hours since 0001-01-01 00:00:00.0"
>>> times.calendar = "gregorian"
</code></pre>
<p>The <code><a title="netCDF4.Dataset.ncattrs" href="#netCDF4.Dataset.ncattrs">Dataset.ncattrs()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>, <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> or
<code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> instance can be used to retrieve the names of all the netCDF
attributes. This method is provided as a convenience, since using the
built-in <code>dir</code> Python function will return a bunch of private methods
and attributes that cannot (or should not) be modified by the user.</p>
<pre><code class="language-python">>>> for name in rootgrp.ncattrs():
... print("Global attr {} = {}".format(name, getattr(rootgrp, name)))
Global attr description = bogus example script
Global attr history = Created Mon Jul 8 14:19:41 2019
Global attr source = netCDF4 python module tutorial
</code></pre>
<p>The <code>__dict__</code> attribute of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>, <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> or <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code>
instance provides all the netCDF attribute name/value pairs in a python
dictionary:</p>
<pre><code class="language-python">>>> print(rootgrp.__dict__)
{'description': 'bogus example script', 'history': 'Created Mon Jul 8 14:19:41 2019', 'source': 'netCDF4 python module tutorial'}
</code></pre>
<p>Attributes can be deleted from a netCDF <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code>, <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> or
<code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> using the python <code>del</code> statement (i.e. <code>del grp.foo</code>
removes the attribute <code>foo</code> the the group <code>grp</code>).</p>
<h2 id="writing-data-to-and-retrieving-data-from-a-netcdf-variable">Writing data to and retrieving data from a netCDF variable</h2>
<p>Now that you have a netCDF <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> instance, how do you put data
into it? You can just treat it like an array and assign data to a slice.</p>
<pre><code class="language-python">>>> import numpy as np
>>> lats = np.arange(-90,91,2.5)
>>> lons = np.arange(-180,180,2.5)
>>> latitudes[:] = lats
>>> longitudes[:] = lons
>>> print("latitudes =\n{}".format(latitudes[:]))
latitudes =
[-90. -87.5 -85. -82.5 -80. -77.5 -75. -72.5 -70. -67.5 -65. -62.5
-60. -57.5 -55. -52.5 -50. -47.5 -45. -42.5 -40. -37.5 -35. -32.5
-30. -27.5 -25. -22.5 -20. -17.5 -15. -12.5 -10. -7.5 -5. -2.5
0. 2.5 5. 7.5 10. 12.5 15. 17.5 20. 22.5 25. 27.5
30. 32.5 35. 37.5 40. 42.5 45. 47.5 50. 52.5 55. 57.5
60. 62.5 65. 67.5 70. 72.5 75. 77.5 80. 82.5 85. 87.5
90. ]
</code></pre>
<p>Unlike NumPy's array objects, netCDF <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code>
objects with unlimited dimensions will grow along those dimensions if you
assign data outside the currently defined range of indices.</p>
<pre><code class="language-python">>>> # append along two unlimited dimensions by assigning to slice.
>>> nlats = len(rootgrp.dimensions["lat"])
>>> nlons = len(rootgrp.dimensions["lon"])
>>> print("temp shape before adding data = {}".format(temp.shape))
temp shape before adding data = (0, 0, 73, 144)
>>>
>>> from numpy.random import uniform
>>> temp[0:5, 0:10, :, :] = uniform(size=(5, 10, nlats, nlons))
>>> print("temp shape after adding data = {}".format(temp.shape))
temp shape after adding data = (5, 10, 73, 144)
>>>
>>> # levels have grown, but no values yet assigned.
>>> print("levels shape after adding pressure data = {}".format(levels.shape))
levels shape after adding pressure data = (10,)
</code></pre>
<p>Note that the size of the levels variable grows when data is appended
along the <code>level</code> dimension of the variable <code>temp</code>, even though no
data has yet been assigned to levels.</p>
<pre><code class="language-python">>>> # now, assign data to levels dimension variable.
>>> levels[:] = [1000.,850.,700.,500.,300.,250.,200.,150.,100.,50.]
</code></pre>
<p>However, that there are some differences between NumPy and netCDF
variable slicing rules. Slices behave as usual, being specified as a
<code>start:stop:step</code> triplet. Using a scalar integer index <code>i</code> takes the ith
element and reduces the rank of the output array by one. Boolean array and
integer sequence indexing behaves differently for netCDF variables
than for numpy arrays.
Only 1-d boolean arrays and integer sequences are
allowed, and these indices work independently along each dimension (similar
to the way vector subscripts work in fortran).
This means that</p>
<pre><code class="language-python">>>> temp[0, 0, [0,1,2,3], [0,1,2,3]].shape
(4, 4)
</code></pre>
<p>returns an array of shape (4,4) when slicing a netCDF variable, but for a
numpy array it returns an array of shape (4,).
Similarly, a netCDF variable of shape <code>(2,3,4,5)</code> indexed
with <code>[0, array([True, False, True]), array([False, True, True, True]), :]</code>
would return a <code>(2, 3, 5)</code> array. In NumPy, this would raise an error since
it would be equivalent to <code>[0, [0,1], [1,2,3], :]</code>. When slicing with integer
sequences, the indices <strong><em>need not be sorted</em></strong> and <strong><em>may contain
duplicates</em></strong> (both of these are new features in version 1.2.1).
While this behaviour may cause some confusion for those used to NumPy's 'fancy indexing' rules,
it provides a very powerful way to extract data from multidimensional netCDF
variables by using logical operations on the dimension arrays to create slices.</p>
<p>For example,</p>
<pre><code class="language-python">>>> tempdat = temp[::2, [1,3,6], lats>0, lons>0]
</code></pre>
<p>will extract time indices 0,2 and 4, pressure levels
850, 500 and 200 hPa, all Northern Hemisphere latitudes and Eastern
Hemisphere longitudes, resulting in a numpy array of shape
(3, 3, 36, 71).</p>
<pre><code class="language-python">>>> print("shape of fancy temp slice = {}".format(tempdat.shape))
shape of fancy temp slice = (3, 3, 36, 71)
</code></pre>
<p><strong><em>Special note for scalar variables</em></strong>: To extract data from a scalar variable
<code>v</code> with no associated dimensions, use <code>numpy.asarray(v)</code> or <code>v[…]</code>.
The result will be a numpy scalar array.</p>
<p>By default, netcdf4-python returns numpy masked arrays with values equal to the
<code>missing_value</code> or <code>_FillValue</code> variable attributes masked for primitive and
enum data types.
The <code><a title="netCDF4.Dataset.set_auto_mask" href="#netCDF4.Dataset.set_auto_mask">Dataset.set_auto_mask()</a></code> <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> and <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> methods
can be used to disable this feature so that
numpy arrays are always returned, with the missing values included. Prior to
version 1.4.0 the default behavior was to only return masked arrays when the
requested slice contained missing values.
This behavior can be recovered
using the <code><a title="netCDF4.Dataset.set_always_mask" href="#netCDF4.Dataset.set_always_mask">Dataset.set_always_mask()</a></code> method. If a masked array is
written to a netCDF variable, the masked elements are filled with the
value specified by the <code>missing_value</code> attribute.
If the variable has
no <code>missing_value</code>, the <code>_FillValue</code> is used instead.</p>
<h2 id="dealing-with-time-coordinates">Dealing with time coordinates</h2>
<p>Time coordinate values pose a special challenge to netCDF users.
Most
metadata standards (such as CF) specify that time should be
measure relative to a fixed date using a certain calendar, with units
specified like <code>hours since YY-MM-DD hh:mm:ss</code>.
These units can be
awkward to deal with, without a utility to convert the values to and
from calendar dates.
The functions <a href="https://unidata.github.io/cftime/api.html">num2date</a>
and <a href="https://unidata.github.io/cftime/api.html">date2num</a> are
provided by <a href="https://unidata.github.io/cftime">cftime</a> to do just that.
Here's an example of how they can be used:</p>
<pre><code class="language-python">>>> # fill in times.
>>> from datetime import datetime, timedelta
>>> from cftime import num2date, date2num
>>> dates = [datetime(2001,3,1)+n*timedelta(hours=12) for n in range(temp.shape[0])]
>>> times[:] = date2num(dates,units=times.units,calendar=times.calendar)
>>> print("time values (in units {}):\n{}".format(times.units, times[:]))
time values (in units hours since 0001-01-01 00:00:00.0):
[17533104. 17533116. 17533128. 17533140. 17533152.]
>>> dates = num2date(times[:],units=times.units,calendar=times.calendar)
>>> print("dates corresponding to time values:\n{}".format(dates))
[cftime.DatetimeGregorian(2001, 3, 1, 0, 0, 0, 0, has_year_zero=False)
cftime.DatetimeGregorian(2001, 3, 1, 12, 0, 0, 0, has_year_zero=False)
cftime.DatetimeGregorian(2001, 3, 2, 0, 0, 0, 0, has_year_zero=False)
cftime.DatetimeGregorian(2001, 3, 2, 12, 0, 0, 0, has_year_zero=False)
cftime.DatetimeGregorian(2001, 3, 3, 0, 0, 0, 0, has_year_zero=False)]
</code></pre>
<p><code><a title="netCDF4.num2date" href="#netCDF4.num2date">num2date()</a></code> converts numeric values of time in the specified <code>units</code>
and <code>calendar</code> to datetime objects, and <code><a title="netCDF4.date2num" href="#netCDF4.date2num">date2num()</a></code> does the reverse.
All the calendars currently defined in the
<a href="http://cfconventions.org">CF metadata convention</a> are supported.
A function called <code><a title="netCDF4.date2index" href="#netCDF4.date2index">date2index()</a></code> is also provided which returns the indices
of a netCDF time variable corresponding to a sequence of datetime instances.</p>
<h2 id="reading-data-from-a-multi-file-netcdf-dataset">Reading data from a multi-file netCDF dataset</h2>
<p>If you want to read data from a variable that spans multiple netCDF files,
you can use the <code><a title="netCDF4.MFDataset" href="#netCDF4.MFDataset">MFDataset</a></code> class to read the data as if it were
contained in a single file. Instead of using a single filename to create
a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> instance, create a <code><a title="netCDF4.MFDataset" href="#netCDF4.MFDataset">MFDataset</a></code> instance with either a list
of filenames, or a string with a wildcard (which is then converted to
a sorted list of files using the python glob module).
Variables in the list of files that share the same unlimited
dimension are aggregated together, and can be sliced across multiple
files.
To illustrate this, let's first create a bunch of netCDF files with
the same variable (with the same unlimited dimension).
The files
must in be in <code>NETCDF3_64BIT_OFFSET</code>, <code>NETCDF3_64BIT_DATA</code>, <code>NETCDF3_CLASSIC</code> or
<code>NETCDF4_CLASSIC</code> format (<code>NETCDF4</code> formatted multi-file
datasets are not supported).</p>
<pre><code class="language-python">>>> for nf in range(10):
... with Dataset("mftest%s.nc" % nf, "w", format="NETCDF4_CLASSIC") as f:
... _ = f.createDimension("x",None)
... x = f.createVariable("x","i",("x",))
... x[0:10] = np.arange(nf*10,10*(nf+1))
</code></pre>
<p>Now read all the files back in at once with <code><a title="netCDF4.MFDataset" href="#netCDF4.MFDataset">MFDataset</a></code></p>
<pre><code class="language-python">>>> from netCDF4 import MFDataset
>>> f = MFDataset("mftest*nc")
>>> print(f.variables["x"][:])
[ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95
96 97 98 99]
</code></pre>
<p>Note that <code><a title="netCDF4.MFDataset" href="#netCDF4.MFDataset">MFDataset</a></code> can only be used to read, not write, multi-file
datasets.</p>
<h2 id="efficient-compression-of-netcdf-variables">Efficient compression of netCDF variables</h2>
<p>Data stored in netCDF <code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> objects can be compressed and
decompressed on the fly. The compression algorithm used is determined
by the <code>compression</code> keyword argument to the <code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> method.
<code>zlib</code> compression is always available, <code>szip</code> is available if the linked HDF5
library supports it, and <code>zstd</code>, <code>bzip2</code>, <code>blosc_lz</code>,<code>blosc_lz4</code>,<code>blosc_lz4hc</code>,
<code>blosc_zlib</code> and <code>blosc_zstd</code> are available via optional external plugins.
The <code>complevel</code> keyword regulates the
speed and efficiency of the compression for <code>zlib</code>, <code>bzip</code> and <code>zstd</code> (1 being fastest, but lowest
compression ratio, 9 being slowest but best compression ratio). The
default value of <code>complevel</code> is 4. Setting <code>shuffle=False</code> will turn
off the HDF5 shuffle filter, which de-interlaces a block of data before
<code>zlib</code> compression by reordering the bytes.
The shuffle filter can
significantly improve compression ratios, and is on by default if <code>compression=zlib</code>.
Setting
<code>fletcher32</code> keyword argument to
<code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> to <code>True</code> (it's <code>False</code> by
default) enables the Fletcher32 checksum algorithm for error detection.
It's also possible to set the HDF5 chunking parameters and endian-ness
of the binary data stored in the HDF5 file with the <code>chunksizes</code>
and <code>endian</code> keyword arguments to
<code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code>.
These keyword arguments only
are relevant for <code>NETCDF4</code> and <code>NETCDF4_CLASSIC</code> files (where the
underlying file format is HDF5) and are silently ignored if the file
format is <code>NETCDF3_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.
If the HDF5 library is built with szip support, compression=<code>szip</code> can also
be used (in conjunction with the <code>szip_coding</code> and <code>szip_pixels_per_block</code> keyword
arguments).</p>
<p>If your data only has a certain number of digits of precision (say for
example, it is temperature data that was measured with a precision of
0.1 degrees), you can dramatically improve compression by
quantizing (or truncating) the data. There are two methods supplied for
doing this.
You can use the <code>least_significant_digit</code>
keyword argument to <code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> to specify
the power of ten of the smallest decimal place in
the data that is a reliable value. For example if the data has a
precision of 0.1, then setting <code>least_significant_digit=1</code> will cause
data the data to be quantized using <code>numpy.around(scale*data)/scale</code>, where
scale = 2**bits, and bits is determined so that a precision of 0.1 is
retained (in this case bits=4).
This is done at the python level and is
not a part of the underlying C library.
Starting with netcdf-c version 4.9.0,
a quantization capability is provided in the library.
This can be
used via the <code>significant_digits</code> <code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> kwarg (new in
version 1.6.0).
The interpretation of <code>significant_digits</code> is different than <code>least_signficant_digit</code>
in that it specifies the absolute number of significant digits independent
of the magnitude of the variable (the floating point exponent).
Either of these approaches makes the compression
'lossy' instead of 'lossless', that is some precision in the data is
sacrificed for the sake of disk space.</p>
<p>In our example, try replacing the line</p>
<pre><code class="language-python">>>> temp = rootgrp.createVariable("temp","f4",("time","level","lat","lon",))
</code></pre>
<p>with</p>
<pre><code class="language-python">>>> temp = rootgrp.createVariable("temp","f4",("time","level","lat","lon",),compression='zlib')
</code></pre>
<p>and then</p>
<pre><code class="language-python">>>> temp = rootgrp.createVariable("temp","f4",("time","level","lat","lon",),compression='zlib',least_significant_digit=3)
</code></pre>
<p>or with netcdf-c >= 4.9.0</p>
<pre><code class="language-python">>>> temp = rootgrp.createVariable("temp","f4",("time","level","lat","lon",),compression='zlib',significant_digits=4)
</code></pre>
<p>and see how much smaller the resulting files are.</p>
<h2 id="beyond-homogeneous-arrays-of-a-fixed-type-compound-data-types">Beyond homogeneous arrays of a fixed type - compound data types</h2>
<p>Compound data types map directly to numpy structured (a.k.a 'record')
arrays.
Structured arrays are akin to C structs, or derived types
in Fortran. They allow for the construction of table-like structures
composed of combinations of other data types, including other
compound types. Compound types might be useful for representing multiple
parameter values at each point on a grid, or at each time and space
location for scattered (point) data. You can then access all the
information for a point by reading one variable, instead of reading
different parameters from different variables.
Compound data types
are created from the corresponding numpy data type using the
<code><a title="netCDF4.Dataset.createCompoundType" href="#netCDF4.Dataset.createCompoundType">Dataset.createCompoundType()</a></code> method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance.
Since there is no native complex data type in netcdf (but see
<a href="#support-for-complex-numbers">Support for complex numbers</a>), compound
types are handy for storing numpy complex arrays. Here's an example:</p>
<pre><code class="language-python">>>> f = Dataset("complex.nc","w")
>>> size = 3 # length of 1-d complex array
>>> # create sample complex data.
>>> datac = np.exp(1j*(1.+np.linspace(0, np.pi, size)))
>>> # create complex128 compound data type.
>>> complex128 = np.dtype([("real",np.float64),("imag",np.float64)])
>>> complex128_t = f.createCompoundType(complex128,"complex128")
>>> # create a variable with this data type, write some data to it.
>>> x_dim = f.createDimension("x_dim",None)
>>> v = f.createVariable("cmplx_var",complex128_t,"x_dim")
>>> data = np.empty(size,complex128) # numpy structured array
>>> data["real"] = datac.real; data["imag"] = datac.imag
>>> v[:] = data # write numpy structured array to netcdf compound var
>>> # close and reopen the file, check the contents.
>>> f.close(); f = Dataset("complex.nc")
>>> v = f.variables["cmplx_var"]
>>> datain = v[:] # read in all the data into a numpy structured array
>>> # create an empty numpy complex array
>>> datac2 = np.empty(datain.shape,np.complex128)
>>> # .. fill it with contents of structured array.
>>> datac2.real = datain["real"]; datac2.imag = datain["imag"]
>>> print('{}: {}'.format(datac.dtype, datac)) # original data
complex128: [ 0.54030231+0.84147098j -0.84147098+0.54030231j -0.54030231-0.84147098j]
>>>
>>> print('{}: {}'.format(datac2.dtype, datac2)) # data from file
complex128: [ 0.54030231+0.84147098j -0.84147098+0.54030231j -0.54030231-0.84147098j]
</code></pre>
<p>Compound types can be nested, but you must create the 'inner'
ones first. All possible numpy structured arrays cannot be
represented as Compound variables - an error message will be
raise if you try to create one that is not supported.
All of the compound types defined for a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> are stored
in a Python dictionary, just like variables and dimensions. As always, printing
objects gives useful summary information in an interactive session:</p>
<pre><code class="language-python">>>> print(f)
<class 'netCDF4._netCDF4.Dataset'>
root group (NETCDF4 data model, file format HDF5):
dimensions(sizes): x_dim(3)
variables(dimensions): {'names':['real','imag'], 'formats':['<f8','<f8'], 'offsets':[0,8], 'itemsize':16, 'aligned':True} cmplx_var(x_dim)
groups:
>>> print(f.variables["cmplx_var"])
<class 'netCDF4._netCDF4.Variable'>
compound cmplx_var(x_dim)
compound data type: {'names':['real','imag'], 'formats':['<f8','<f8'], 'offsets':[0,8], 'itemsize':16, 'aligned':True}
unlimited dimensions: x_dim
current shape = (3,)
>>> print(f.cmptypes)
{'complex128': <class 'netCDF4._netCDF4.CompoundType'>: name = 'complex128', numpy dtype = {'names':['real','imag'], 'formats':['<f8','<f8'], 'offsets':[0,8], 'itemsize':16, 'aligned':True}}
>>> print(f.cmptypes["complex128"])
<class 'netCDF4._netCDF4.CompoundType'>: name = 'complex128', numpy dtype = {'names':['real','imag'], 'formats':['<f8','<f8'], 'offsets':[0,8], 'itemsize':16, 'aligned':True}
</code></pre>
<h2 id="variable-length-vlen-data-types">Variable-length (vlen) data types</h2>
<p>NetCDF 4 has support for variable-length or "ragged" arrays.
These are arrays
of variable length sequences having the same type. To create a variable-length
data type, use the <code><a title="netCDF4.Dataset.createVLType" href="#netCDF4.Dataset.createVLType">Dataset.createVLType()</a></code> method
method of a <code><a title="netCDF4.Dataset" href="#netCDF4.Dataset">Dataset</a></code> or <code><a title="netCDF4.Group" href="#netCDF4.Group">Group</a></code> instance.</p>
<pre><code class="language-python">>>> f = Dataset("tst_vlen.nc","w")
>>> vlen_t = f.createVLType(np.int32, "phony_vlen")
</code></pre>
<p>The numpy datatype of the variable-length sequences and the name of the
new datatype must be specified. Any of the primitive datatypes can be
used (signed and unsigned integers, 32 and 64 bit floats, and characters),
but compound data types cannot.
A new variable can then be created using this datatype.</p>
<pre><code class="language-python">>>> x = f.createDimension("x",3)
>>> y = f.createDimension("y",4)
>>> vlvar = f.createVariable("phony_vlen_var", vlen_t, ("y","x"))
</code></pre>
<p>Since there is no native vlen datatype in numpy, vlen arrays are represented
in python as object arrays (arrays of dtype <code>object</code>). These are arrays whose
elements are Python object pointers, and can contain any type of python object.
For this application, they must contain 1-D numpy arrays all of the same type
but of varying length.
In this case, they contain 1-D numpy <code>int32</code> arrays of random length between
1 and 10.</p>
<pre><code class="language-python">>>> import random
>>> random.seed(54321)
>>> data = np.empty(len(y)*len(x),object)
>>> for n in range(len(y)*len(x)):
... data[n] = np.arange(random.randint(1,10),dtype="int32")+1
>>> data = np.reshape(data,(len(y),len(x)))
>>> vlvar[:] = data
>>> print("vlen variable =\n{}".format(vlvar[:]))
vlen variable =
[[array([1, 2, 3, 4, 5, 6, 7, 8], dtype=int32) array([1, 2], dtype=int32)
array([1, 2, 3, 4], dtype=int32)]
[array([1, 2, 3], dtype=int32)
array([1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=int32)
array([1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=int32)]
[array([1, 2, 3, 4, 5, 6, 7], dtype=int32) array([1, 2, 3], dtype=int32)
array([1, 2, 3, 4, 5, 6], dtype=int32)]
[array([1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=int32)
array([1, 2, 3, 4, 5], dtype=int32) array([1, 2], dtype=int32)]]
>>> print(f)
<class 'netCDF4._netCDF4.Dataset'>
root group (NETCDF4 data model, file format HDF5):
dimensions(sizes): x(3), y(4)
variables(dimensions): int32 phony_vlen_var(y,x)
groups:
>>> print(f.variables["phony_vlen_var"])
<class 'netCDF4._netCDF4.Variable'>
vlen phony_vlen_var(y, x)
vlen data type: int32
unlimited dimensions:
current shape = (4, 3)
>>> print(f.vltypes["phony_vlen"])
<class 'netCDF4._netCDF4.VLType'>: name = 'phony_vlen', numpy dtype = int32
</code></pre>
<p>Numpy object arrays containing python strings can also be written as vlen
variables,
For vlen strings, you don't need to create a vlen data type.
Instead, simply use the python <code>str</code> builtin (or a numpy string datatype
with fixed length greater than 1) when calling the
<code><a title="netCDF4.Dataset.createVariable" href="#netCDF4.Dataset.createVariable">Dataset.createVariable()</a></code> method.</p>
<pre><code class="language-python">>>> z = f.createDimension("z",10)
>>> strvar = f.createVariable("strvar", str, "z")
</code></pre>
<p>In this example, an object array is filled with random python strings with
random lengths between 2 and 12 characters, and the data in the object
array is assigned to the vlen string variable.</p>
<pre><code class="language-python">>>> chars = "1234567890aabcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
>>> data = np.empty(10,"O")
>>> for n in range(10):
... stringlen = random.randint(2,12)
... data[n] = "".join([random.choice(chars) for i in range(stringlen)])
>>> strvar[:] = data
>>> print("variable-length string variable:\n{}".format(strvar[:]))
variable-length string variable:
['Lh' '25F8wBbMI' '53rmM' 'vvjnb3t63ao' 'qjRBQk6w' 'aJh' 'QF'
'jtIJbJACaQk4' '3Z5' 'bftIIq']
>>> print(f)
<class 'netCDF4._netCDF4.Dataset'>
root group (NETCDF4 data model, file format HDF5):
dimensions(sizes): x(3), y(4), z(10)
variables(dimensions): int32 phony_vlen_var(y,x), <class 'str'> strvar(z)
groups:
>>> print(f.variables["strvar"])
<class 'netCDF4._netCDF4.Variable'>
vlen strvar(z)
vlen data type: <class 'str'>
unlimited dimensions:
current shape = (10,)
</code></pre>
<p>It is also possible to set contents of vlen string variables with numpy arrays
of any string or unicode data type. Note, however, that accessing the contents
of such variables will always return numpy arrays with dtype <code>object</code>.</p>
<h2 id="enum-data-type">Enum data type</h2>
<p>netCDF4 has an enumerated data type, which is an integer datatype that is
restricted to certain named values. Since Enums don't map directly to
a numpy data type, they are read and written as integer arrays.</p>
<p>Here's an example of using an Enum type to hold cloud type data.
The base integer data type and a python dictionary describing the allowed
values and their names are used to define an Enum data type using
<code><a title="netCDF4.Dataset.createEnumType" href="#netCDF4.Dataset.createEnumType">Dataset.createEnumType()</a></code>.</p>
<pre><code class="language-python">>>> nc = Dataset('clouds.nc','w')
>>> # python dict with allowed values and their names.
>>> enum_dict = {'Altocumulus': 7, 'Missing': 255,
... 'Stratus': 2, 'Clear': 0,
... 'Nimbostratus': 6, 'Cumulus': 4, 'Altostratus': 5,
... 'Cumulonimbus': 1, 'Stratocumulus': 3}
>>> # create the Enum type called 'cloud_t'.
>>> cloud_type = nc.createEnumType(np.uint8,'cloud_t',enum_dict)
>>> print(cloud_type)
<class 'netCDF4._netCDF4.EnumType'>: name = 'cloud_t', numpy dtype = uint8, fields/values ={'Altocumulus': 7, 'Missing': 255, 'Stratus': 2, 'Clear': 0, 'Nimbostratus': 6, 'Cumulus': 4, 'Altostratus': 5, 'Cumulonimbus': 1, 'Stratocumulus': 3}
</code></pre>
<p>A new variable can be created in the usual way using this data type.
Integer data is written to the variable that represents the named
cloud types in enum_dict. A <code>ValueError</code> will be raised if an attempt
is made to write an integer value not associated with one of the
specified names.</p>
<pre><code class="language-python">>>> time = nc.createDimension('time',None)
>>> # create a 1d variable of type 'cloud_type'.
>>> # The fill_value is set to the 'Missing' named value.
>>> cloud_var = nc.createVariable('primary_cloud',cloud_type,'time',
... fill_value=enum_dict['Missing'])
>>> # write some data to the variable.
>>> cloud_var[:] = [enum_dict[k] for k in ['Clear', 'Stratus', 'Cumulus',
... 'Missing', 'Cumulonimbus']]
>>> nc.close()
>>> # reopen the file, read the data.
>>> nc = Dataset('clouds.nc')
>>> cloud_var = nc.variables['primary_cloud']
>>> print(cloud_var)
<class 'netCDF4._netCDF4.Variable'>
enum primary_cloud(time)
_FillValue: 255
enum data type: uint8
unlimited dimensions: time
current shape = (5,)
>>> print(cloud_var.datatype.enum_dict)
{'Altocumulus': 7, 'Missing': 255, 'Stratus': 2, 'Clear': 0, 'Nimbostratus': 6, 'Cumulus': 4, 'Altostratus': 5, 'Cumulonimbus': 1, 'Stratocumulus': 3}
>>> print(cloud_var[:])
[0 2 4 -- 1]
>>> nc.close()
</code></pre>
<h2 id="parallel-io">Parallel IO</h2>
<p>If MPI parallel enabled versions of netcdf and hdf5 or pnetcdf are detected,
and <a href="https://mpi4py.scipy.org">mpi4py</a> is installed, netcdf4-python will
be built with parallel IO capabilities enabled. Parallel IO of NETCDF4 or
NETCDF4_CLASSIC formatted files is only available if the MPI parallel HDF5
library is available. Parallel IO of classic netcdf-3 file formats is only
available if the <a href="https://parallel-netcdf.github.io/">PnetCDF</a> library is
available. To use parallel IO, your program must be running in an MPI
environment using <a href="https://mpi4py.scipy.org">mpi4py</a>.</p>
<pre><code class="language-python">>>> from mpi4py import MPI
>>> import numpy as np
>>> from netCDF4 import Dataset
>>> rank = MPI.COMM_WORLD.rank # The process ID (integer 0-3 for 4-process run)
</code></pre>
<p>To run an MPI-based parallel program like this, you must use <code>mpiexec</code> to launch several
parallel instances of Python (for example, using <code>mpiexec -np 4 python mpi_example.py</code>).
The parallel features of netcdf4-python are mostly transparent -
when a new dataset is created or an existing dataset is opened,
use the <code>parallel</code> keyword to enable parallel access.</p>
<pre><code class="language-python">>>> nc = Dataset('parallel_test.nc','w',parallel=True)
</code></pre>
<p>The optional <code>comm</code> keyword may be used to specify a particular
MPI communicator (<code>MPI_COMM_WORLD</code> is used by default).
Each process (or rank)
can now write to the file independently.
In this example the process rank is
written to a different variable index on each task</p>
<pre><code class="language-python">>>> d = nc.createDimension('dim',4)
>>> v = nc.createVariable('var', np.int64, 'dim')
>>> v[rank] = rank
>>> nc.close()
% ncdump parallel_test.nc
netcdf parallel_test {
dimensions:
dim = 4 ;
variables:
int64 var(dim) ;
data:
var = 0, 1, 2, 3 ;
}
</code></pre>
<p>There are two types of parallel IO, independent (the default) and collective.
Independent IO means that each process can do IO independently. It should not
depend on or be affected by other processes. Collective IO is a way of doing
IO defined in the MPI-IO standard; unlike independent IO, all processes must
participate in doing IO. To toggle back and forth between
the two types of IO, use the <code><a title="netCDF4.Variable.set_collective" href="#netCDF4.Variable.set_collective">Variable.set_collective()</a></code>
<code><a title="netCDF4.Variable" href="#netCDF4.Variable">Variable</a></code> method. All metadata
operations (such as creation of groups, types, variables, dimensions, or attributes)
are collective.
There are a couple of important limitations of parallel IO:</p>
<ul>
<li>parallel IO for NETCDF4 or NETCDF4_CLASSIC formatted files is only available
if the netcdf library was compiled with MPI enabled HDF5.</li>
<li>parallel IO for all classic netcdf-3 file formats is only available if the
netcdf library was compiled with <a href="https://parallel-netcdf.github.io">PnetCDF</a>.</li>
<li>If a variable has an unlimited dimension, appending data must be done in collective mode.
If the write is done in independent mode, the operation will fail with a
a generic "HDF Error".</li>
<li>You can write compressed data in parallel only with netcdf-c >= 4.7.4
and hdf5 >= 1.10.3 (although you can read in parallel with earlier versions). To write
compressed data in parallel, the variable must be in 'collective IO mode'.
This is done
automatically on variable creation if compression is turned on, but if you are appending
to a variable in an existing file, you must use <code><a title="netCDF4.Variable.set_collective" href="#netCDF4.Variable.set_collective">Variable.set_collective()</a>(True)</code> before attempting
to write to it.</li>
<li>You cannot use variable-length (VLEN) data types.</li>
</ul>
<h2 id="dealing-with-strings">Dealing with strings</h2>
<p>The most flexible way to store arrays of strings is with the
<a href="#variable-length-vlen-data-type">Variable-length (vlen) string data type</a>. However, this requires
the use of the NETCDF4 data model, and the vlen type does not map very well
numpy arrays (you have to use numpy arrays of dtype=<code>object</code>, which are arrays of
arbitrary python objects). numpy does have a fixed-width string array
data type, but unfortunately the netCDF data model does not.
Instead fixed-width byte strings are typically stored as <a href="https://www.unidata.ucar.edu/software/netcdf/docs/BestPractices.html#bp_Strings-and-Variables-of-type-char">arrays of 8-bit
characters</a>.
To perform the conversion to and from character arrays to fixed-width numpy string arrays, the
following convention is followed by the python interface.
If the <code>_Encoding</code> special attribute is set for a character array
(dtype <code>S1</code>) variable, the <code><a title="netCDF4.chartostring" href="#netCDF4.chartostring">chartostring()</a></code> utility function is used to convert the array of
characters to an array of strings with one less dimension (the last dimension is
interpreted as the length of each string) when reading the data. The character
set (usually ascii) is specified by the <code>_Encoding</code> attribute. If <code>_Encoding</code>
is 'none' or 'bytes', then the character array is converted to a numpy
fixed-width byte string array (dtype <code>S#</code>), otherwise a numpy unicode (dtype
<code>U#</code>) array is created.
When writing the data,
<code><a title="netCDF4.stringtochar" href="#netCDF4.stringtochar">stringtochar()</a></code> is used to convert the numpy string array to an array of
characters with one more dimension. For example,</p>
<pre><code class="language-python">>>> from netCDF4 import stringtochar
>>> nc = Dataset('stringtest.nc','w',format='NETCDF4_CLASSIC')
>>> _ = nc.createDimension('nchars',3)
>>> _ = nc.createDimension('nstrings',None)
>>> v = nc.createVariable('strings','S1',('nstrings','nchars'))
>>> datain = np.array(['foo','bar'],dtype='S3')
>>> v[:] = stringtochar(datain) # manual conversion to char array
>>> print(v[:]) # data returned as char array
[[b'f' b'o' b'o']
[b'b' b'a' b'r']]
>>> v._Encoding = 'ascii' # this enables automatic conversion
>>> v[:] = datain # conversion to char array done internally
>>> print(v[:]) # data returned in numpy string array
['foo' 'bar']
>>> nc.close()
</code></pre>
<p>Even if the <code>_Encoding</code> attribute is set, the automatic conversion of char
arrays to/from string arrays can be disabled with
<code><a title="netCDF4.Variable.set_auto_chartostring" href="#netCDF4.Variable.set_auto_chartostring">Variable.set_auto_chartostring()</a></code>.</p>
<p>A similar situation is often encountered with numpy structured arrays with subdtypes
containing fixed-wdith byte strings (dtype=<code>S#</code>). Since there is no native fixed-length string
netCDF datatype, these numpy structure arrays are mapped onto netCDF compound
types with character array elements.
In this case the string <-> char array
conversion is handled automatically (without the need to set the <code>_Encoding</code>
attribute) using <a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.view.html">numpy
views</a>.
The structured array dtype (including the string elements) can even be used to
define the compound data type - the string dtype will be converted to