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/*! \page tutorial.dox The NetCDF-C Tutorial
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\brief The NetCDF-C Tutorial
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\tableofcontents
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\section sec_tut Tutorial Documentation
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This page contains references to various other NetCDF background and tutorial pages.
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\subsection tutorial_pages Tutorial Pages
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- \subpage netcdf_working_with_netcdf_files
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- \subpage tutorial_ncids
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- \subpage creating
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- \subpage reading_known
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- \subpage reading_unknown
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- \subpage accessing_subsets
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\subsection background_further_reading Background and Further Reading
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- \ref what_is_netcdf
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- \subpage netcdf_documentation
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\subsection sub_sec_netcdf_data_model NetCDF Data Model:
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- \subpage netcdf_data_model
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- \ref classic_model
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- \ref enhanced_model
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- \subpage unlimited_dims
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- \subpage groups
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- \subpage user_defined_types
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- \subpage string_type
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\subsection sub_sec_important_conventions Important Conventions:
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- \subpage fill_values
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\subsection sub_sec_tools_for_netcdf Tools for NetCDF:
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- \ref netcdf_utilities
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- \ref external_netcdf_tools
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\subsection sub_sec_programming_with_netcdf Programming with NetCDF:
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- \subpage netcdf_apis
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- \subpage error_handling
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- \subpage interoperability_hdf5
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- \subpage parallel_io
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\subsection sub_sec_example_programs Example Programs:
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- \subpage examples1
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\page netcdf_working_with_netcdf_files Working with NetCDF Files from the command line.
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\brief Options for working with netcdf-formatted files from the command line or with an external program.
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\tableofcontents
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\section netcdf_utilities The NetCDF Utilities
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The ncdump command reads a netCDF file and outputs text in a format
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called CDL. The ncgen command reads a text file in CDL format, and
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generates a netCDF data file. The nccopy command copies a netCDF file
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from one binary format to another, optionally changing compression and
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chunksize settings.
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\subsection netcdf_utilities_ncdump ncdump
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The utility ncdump can be used to show the contents of netCDF
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files. By default, ncdump shows the CDL description of the file. This
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CDL description can be fed into ncgen to create the data file.
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See also: \ref ncdump_guide
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\subsection netcdf_utilities_ncgen ncgen
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The ncgen utility can take an ASCII input file, in CDL format, and
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generate a binary netCDF file. It is the opposite of ncdump.
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See also:
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- \ref guide_ncgen
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- \ref guide_ncgen3
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\subsection netcdf_utilities_nccopy nccopy
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The nccopy utility can copy a netCDF file, changing binary format,
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chunk sizes, compression, and other storage settings.
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See also: \ref guide_nccopy
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\section external_netcdf_tools Tools for Manipulating NetCDF Files
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Many existing 3rd-party software applications can read and manipulate netCDF
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files. Before writing your own program, check to see if any existing
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programs meet your needs.
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Three utilities come with the netCDF distribution: ncdump, ncgen, and
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nccopy. (See \ref netcdf_utilities).
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The following general-purpose tools have been found to be useful in
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many situations. Some of the tools on this list are developed at
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Unidata. The others are developed elsewhere, and we can make no
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guarantees about their continued availability or success. All of these
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tools are open-source.
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- <a href="http://www.unidata.ucar.edu/software/udunits">UDUNITS</a> - Unidata library to help with scientific units.
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- <a href="http://www.unidata.ucar.edu/software/idv">IDV</a> - Unidata's Integrated Data Viewer, a 3D visualization and analysis package (Java based).
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- <a href="http://www.ncl.ucar.edu">NCL</a> - NCAR Command Language, a graphics and data manipulation package.
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- <a href="http://grads.iges.org/grads/grads.html">GrADS</a> - The Grid Analysis and Display System package.
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- <a href="http://nco.sourceforge.net">NCO</a> - NetCDF Command line Operators, tools to manipulate netCDF files.
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A <a href="http://www.unidata.ucar.edu/netcdf/software.html">list of
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netCDF tools</a> that we know about can be found on the website. If
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you know of any that should be added to this list, send email to
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support-netcdf@unidata.ucar.edu.
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\page netcdf_apis The NetCDF Programming APIs
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Unidata supports netCDF APIs in C, C++, Fortran 77, Fortran 90, and
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Java.
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The <a href="http://www.unidata.ucar.edu/software/netcdf-java">netCDF
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Java</a> API is a complete implementation of netCDF in Java. It is
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distributed independently of the other APIs. If you are writing web
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server software, you should certainly be doing so in Java.
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The main netCDF distribution contains the C library and the netCDF
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utilities, ncgen/ncdump/nccopy.
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The C++, Fortran 77 and Fortran 90 APIs are distributed separately
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from the C library. The C library must be installed before any of
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these APIs may be built. They depend on the C API.
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Due to the nature of C++ and Fortran 90, users of those languages can
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also use the C and Fortran 77 APIs (respectively) directly.
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Full documentation exists for each API (see \ref
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netcdf_documentation).
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In addition, many other language APIs exist, including Perl, Python,
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and Ruby. Most of these APIs were written and supported by netCDF
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users. Some of them are listed on
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the <a href="http://www.unidata.ucar.edu/netcdf/software.html">netCDF
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software page</a>. Since these generally use the C API, they should
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work well with netCDF-4/HDF5 files, but the maintainers of the APIs
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must add support for netCDF-4 advanced features.
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In addition to the main netCDF-3 C API, there is an additional (older)
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C API, the netCDF-2 API. This API produces exactly the same files as
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the netCDF-3 API - only the API is different. (That is, users can
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create either classic format files, the default, or 64-bit offset
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files, or netCDF-4/HDF5 files.)
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The version 2 API was the API before netCDF-3.0 came out. It is still
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fully supported, however. Programs written to the version 2 API will
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continue to work. The version 2 API is built with the netCDF library
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by default.
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Users writing new programs should use the netCDF-3 API, which contains
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better type checking, better error handling, and better documentation.
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The netCDF-2 API is provided for backward compatibility. Documentation
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for the netCDF-2 API can be found on the netCDF website, see
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http://www.unidata.ucar.edu/netcdf/old_docs/really_old/guide_toc.html.
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\page netcdf_documentation NetCDF Documentation
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Language specific programming guides are available for netCDF for the
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C, C++, Fortran 77, Fortran 90, and Java APIs:
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- C - The NetCDF C Interface Guide.
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- C++ - The NetCDF C++ Interface Guide.
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- Fortran 77 - The NetCDF Fortran 77 Interface Guide.
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- Fortran 90 - The NetCDF Fortran 90 Interface Guide.
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- Java <a href="http://www.unidata.ucar.edu/software/netcdf-java/v2.1/NetcdfJavaUserManual.htm">The netCDF-Java Users Guide</a>.
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Man pages for the C, F77, and F90 interfaces, and ncgen and ncdump,
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are available on the documentation page of the netCDF web site
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(http://www.unidata.ucar.edu/netcdf/docs), and are installed with the
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libraries.
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The latest version of all netCDF documentation can always be found at
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the <a href="http://www.unidata.ucar.edu/netcdf/docs">netCDF
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documentation page</a>.
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\page netcdf_data_model The NetCDF Data Model
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\tableofcontents
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The netCDF data model is the way that we think about data. The data
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model of dimensions, variables, and attributes, which define the \ref
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classic_model, was extended starting with netCDF-4.0. The new \ref
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enhanced_model supports the classic model in a completely
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backward-compatible way, while allowing access to new features such as
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groups, multiple unlimited dimensions, and new types, including
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user-defined types.
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For maximum interoparability with existing code, new data should be
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created with the \ref classic_model.
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<p>\image html nc4-model.png "The NetCDF Enhanced Data Model"
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\section classic_model The Classic Model
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The classic netCDF data model consists of variables, dimensions, and
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attributes. This way of thinking about data was introduced with the
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very first netCDF release, and is still the core of all netCDF files.
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<p>
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\image html nc-classic-uml.png "NetCDF Classic Data Model"
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In version 4.0, the netCDF data model has been expanded. See \ref
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enhanced_model.
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<table>
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<tr><td>
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Variables
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</td><td>
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N-dimensional arrays of data. Variables in netCDF files can be one
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of six types (char, byte, short, int, float, double).
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</td></tr>
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<tr><td>
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Dimensions
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</td><td>
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describe the axes of the data arrays. A dimension has a name and a
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length. An unlimited dimension has a length that can be expanded at
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any time, as more data are written to it. NetCDF files can contain at
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most one unlimited dimension.
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</td></tr>
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<tr><td>
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Attributes
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</td><td>
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annotate variables or files with small notes or supplementary
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metadata. Attributes are always scalar values or 1D arrays, which can
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be associated with either a variable or the file as a whole. Although
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there is no enforced limit, the user is expected to keep attributes
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small.
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</td></tr>
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</table>
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\section enhanced_model The Enhanced Data Model
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With netCDF-4, the netCDF data model has been extended, in a backwards
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compatible way.
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The new data model, which is known as the “Common Data Model” is part
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of an effort here at Unidata to find a common engineering language for
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the development of scientific data solutions. It contains the
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variables, dimensions, and attributes of the classic data model, but
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adds:
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<ul>
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<li>groups - A way of hierarchically organizing data, similar to
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directories in a Unix file system.
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<li>user-defined types - The user can now define compound types
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(like C structures), enumeration types, variable length arrays, and
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opaque types.
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</ul>
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These features may only be used when working with a netCDF-4/HDF5
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file. Files created in classic or 64-bit offset format cannot support
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groups or user-defined types (see \ref netcdf_format).
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<p>\image html nc4-model.png
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With netCDF-4/HDF5 files, the user may define groups, which may
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contain variables, dimensions, and attributes. In this way, a group
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acts as a container for the classic netCDF dataset. But netCDF-4/HDF5
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files can have many groups, organized hierarchically.
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Each file begins with at least one group, the root group. The user may
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then add more groups, receiving a new ncid for each group created.
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Since each group functions as a complete netCDF classic dataset, it is
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possible to have variables with the same name in two or more different
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groups, within the same netCDF-4/HDF5 data file.
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Dimensions have a special scope: they may be seen by all variables in
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their group, and all descendant groups. This allows the user to define
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dimensions in a top-level group, and use them in many sub-groups.
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Since it may be necessary to write code which works with all types of
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netCDF data files, we also introduce the ability to create
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netCDF-4/HDF5 files which follow all the rules of the classic netCDF
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model. That is, these files are in HDF5, but will not support multiple
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unlimited dimensions, user-defined types, groups, etc. They act just
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like a classic netCDF file.
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\section met_example Meteorological Example
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NetCDF can be used to store many kinds of data, but it was originally
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developed for the Earth science community.
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NetCDF views the world of scientific data in the same way that an
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atmospheric scientist might: as sets of related arrays. There are
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various physical quantities (such as pressure and temperature) located
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at points at a particular latitude, longitude, vertical level, and
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time.
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A scientist might also like to store supporting information, such as
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the units, or some information about how the data were produced.
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The axis information (latitude, longitude, level, and time) would be
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stored as netCDF dimensions. Dimensions have a length and a name.
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The physical quantities (pressure, temperature) would be stored as
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netCDF variables. Variables are N-dimensional arrays of data, with a
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name and an associated set of netCDF dimensions.
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It is also customary to add one variable for each dimension, to hold
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the values along that axis. These variables are called “coordinate
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variables.” The latitude coordinate variable would be a
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one-dimensional variable (with latitude as its dimension), and it
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would hold the latitude values at each point along the axis.
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The additional bits of metadata would be stored as netCDF attributes.
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Attributes are always single values or one-dimensional arrays. (This
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works out well for a string, which is a one-dimensional array of ASCII
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characters.)
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The pres_temp_4D_wr.c/pres_temp_4D_rd.c examples show
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how to write and read a file containing some four-dimensional pressure
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and temperature data, including all the metadata needed.
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\page fill_values Fill Values
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Sometimes there are missing values in the data, and some value is
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needed to represent them.
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For example, what value do you put in a sea-surface temperature
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variable for points over land?
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In netCDF, you can create an attribute for the variable (and of the
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same type as the variable) called “_FillValue” that contains a value
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that you have used for missing data. Applications that read the data
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file can use this to know how to represent these values.
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Using attributes it is possible to capture metadata that would
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otherwise be separated from the data. Various conventions have been
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established. By using a set of conventions, a data producer is more
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likely to produce files that can be easily shared within the research
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community, and that contain enough details to be useful as a long-term
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archive. Conventions also make it easier to develop software that
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interprets information represented in data, because a convention
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selects one conventional way to represent information when multiple
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equivalent representations are possible.
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For more information on _FillValue and other attribute conventions,
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see \ref attribute_conventions.
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Climate and meteorological users are urged to follow the Climate and
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Forecast (CF) metadata conventions when producing data files. For more
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information about the CF conventions, see http://cf-pcmdi.llnl.gov.
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\page error_handling Error Handling
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\addtogroup error
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Each netCDF function in the C, Fortran 77, and Fortran 90 APIs returns
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0 on success, in the tradition of C.
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When programming with netCDF in these languages, always check return
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values of every netCDF API call. The return code can be looked up in
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netcdf.h (for C programmers) or netcdf.inc (for Fortran programmers),
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or you can use the strerror function to print out an error
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message. (See nc_strerror/NF_STRERROR/NF90_STRERROR).
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In general, if a function returns an error code, you can assume it
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didn't do what you hoped it would. The exception is the NC_ERANGE
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error, which is returned by any of the reading or writing functions
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when one or more of the values read or written exceeded the range for
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the type. (For example if you were to try to read 1000 into an
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unsigned byte.)
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In the case of NC_ERANGE errors, the netCDF library completes the
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read/write operation, and then returns the error. The type conversion
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is handled like a C type conversion, whether or not it is within
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range. This may yield bad data, but the netCDF library just returns
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NC_ERANGE and leaves it up to the user to handle. (For more
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information about type conversion see Type Conversion).
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\page unlimited_dims Unlimited Dimensions
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Sometimes you don't know the size of all dimensions when you create a
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file, or you would like to arbitrarily extend the file along one of
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the dimensions.
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For example, model output usually has a time dimension. Rather than
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specifying that there will be forty-two output times when creating the
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file, you might like to create it with one time, and then add data for
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additional times, until you wanted to stop.
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For this purpose netCDF provides the unlimited dimension. By
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specifying a length of “unlimited” when defining a dimension, you
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indicate to netCDF that the dimension may be extended, and its length
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may increase.
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In netCDF classic files, there can only be one unlimited dimension,
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and it must be declared first in the list of dimensions for a
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variable.
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For programmers, the unlimited dimension will correspond with the
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slowest-varying dimension. In C this is the first dimension of an
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array, in Fortran, the last.
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The third example in this tutorial, pres_temp_4D, demonstrates how to
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write and read data one time step at a time along an unlimited
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dimension in a classic netCDF file. See pres_temp_4D.
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In netCDF-4/HDF5 files, any number of unlimited dimensions may be
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used, and there is no restriction as to where they appear in a
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variable's list of dimension IDs.
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\page examples1 NetCDF Example Programs
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\tableofcontents
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The netCDF example programs show how to use netCDF.
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In the netCDF distribution, the “examples” directory contains examples
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in C and CDL. The examples create, and then read, example data files
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of increasing complexity.
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There are three sets of netCDF classic example programs; corresponding
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examples are included with the netCDF Fortran and C++ APIs.
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- \ref example_simple_xy
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- \ref example_sfc_pres_temp
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- \ref example_pres_temp_4D
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Any existing netCDF applications can be converted to generate
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netCDF-4/HDF5 files. Simply change the file creation call to include
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the correct mode flag.
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In one of the netCDF classic examples which write a data file, change
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the nc_create() call so that ::NC_NETCDF4 is one of the flags set on
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the create.
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The corresponding read example will work without modification; netCDF
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will notice that the file is a NetCDF-4/HDF5 file, and will read it
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automatically, just as if it were a netCDF classic format file.
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In the example in this section we show some of the advanced features
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of netCDF-4.
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- \ref example_simple_nc4
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- \ref example_simple_xy_nc4
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The examples are built and run with the “make check” command. (See
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\ref building).
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The corresponding examples in each language create identical netCDF
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data files. For example, the C program sfc_pres_temp_wr.c produces the
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same data file as the Fortran 77 program sfc_pres_temp_wr.f.
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\section example_simple_xy The simple_xy Example
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This example is an unrealistically simple netCDF file, to demonstrate
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the minimum operation of the netCDF APIs. Users should seek to make
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their netCDF files more self-describing than this primitive example.
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- simple_xy_wr.c
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- simple_xy_rd.c
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As in all the netCDF tutorial examples, this example file can be
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created by C and by ncgen, which creates it from a CDL script. Both
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ncgen and the C example create identical files, “simple_xy.nc.”
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The simple_xy.nc data file contains two dimensions, “x” and “y”, and
|
|
one netCDF variable, “data.”
|
|
|
|
The CDL for this example is shown below. For more information on
|
|
ncdump and ncgen see NetCDF Utilities.
|
|
|
|
\code
|
|
netcdf simple_xy {
|
|
dimensions:
|
|
x = 6 ;
|
|
y = 12 ;
|
|
variables:
|
|
int data(x, y) ;
|
|
data:
|
|
|
|
data =
|
|
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 ;
|
|
}
|
|
\endcode
|
|
|
|
\section example_sfc_pres_temp The sfc_pres_temp Example
|
|
|
|
This example has been constructed for the meteorological mind.
|
|
|
|
Suppose you have some data you want to write to a netCDF file. For
|
|
example, you have one time step of surface temperature and surface
|
|
pressure, on a 6 x 12 latitude longitude grid.
|
|
|
|
To store this in netCDF, create a file, add two dimensions (latitude
|
|
and longitude) and two variables (pressure and temperature).
|
|
- sfc_pres_temp_wr.c
|
|
- sfc_pres_temp_rd.c
|
|
|
|
In this example we add some netCDF attributes, as is typical in
|
|
scientific applications, to further describe the data. In this case we
|
|
add a units attribute to every netCDF variable.
|
|
|
|
In this example we also add additional netCDF variables to describe
|
|
the coordinate system. These “coordinate variables” allow us to
|
|
specify the latitudes and longitudes that describe the data grid.
|
|
|
|
The CDL version of the data file, generated by ncdump, is shown below
|
|
(see \ref netcdf_utilities).
|
|
|
|
\code
|
|
netcdf sfc_pres_temp {
|
|
dimensions:
|
|
latitude = 6 ;
|
|
longitude = 12 ;
|
|
variables:
|
|
float latitude(latitude) ;
|
|
latitude:units = "degrees_north" ;
|
|
float longitude(longitude) ;
|
|
longitude:units = "degrees_east" ;
|
|
float pressure(latitude, longitude) ;
|
|
pressure:units = "hPa" ;
|
|
float temperature(latitude, longitude) ;
|
|
temperature:units = "celsius" ;
|
|
data:
|
|
|
|
latitude = 25, 30, 35, 40, 45, 50 ;
|
|
|
|
longitude = -125, -120, -115, -110, -105, -100, -95, -90, -85, -80, -75, -70 ;
|
|
|
|
pressure =
|
|
900, 906, 912, 918, 924, 930, 936, 942, 948, 954, 960, 966,
|
|
901, 907, 913, 919, 925, 931, 937, 943, 949, 955, 961, 967,
|
|
902, 908, 914, 920, 926, 932, 938, 944, 950, 956, 962, 968,
|
|
903, 909, 915, 921, 927, 933, 939, 945, 951, 957, 963, 969,
|
|
904, 910, 916, 922, 928, 934, 940, 946, 952, 958, 964, 970,
|
|
905, 911, 917, 923, 929, 935, 941, 947, 953, 959, 965, 971 ;
|
|
|
|
temperature =
|
|
9, 10.5, 12, 13.5, 15, 16.5, 18, 19.5, 21, 22.5, 24, 25.5,
|
|
9.25, 10.75, 12.25, 13.75, 15.25, 16.75, 18.25, 19.75, 21.25, 22.75, 24.25,
|
|
25.75,
|
|
9.5, 11, 12.5, 14, 15.5, 17, 18.5, 20, 21.5, 23, 24.5, 26,
|
|
9.75, 11.25, 12.75, 14.25, 15.75, 17.25, 18.75, 20.25, 21.75, 23.25, 24.75,
|
|
26.25,
|
|
10, 11.5, 13, 14.5, 16, 17.5, 19, 20.5, 22, 23.5, 25, 26.5,
|
|
10.25, 11.75, 13.25, 14.75, 16.25, 17.75, 19.25, 20.75, 22.25, 23.75,
|
|
25.25, 26.75 ;
|
|
}
|
|
\endcode
|
|
|
|
\section example_pres_temp_4D The pres_temp_4D Example
|
|
|
|
This example expands on the previous example by making our
|
|
two-dimensional data into four-dimensional data, adding a vertical
|
|
level axis and an unlimited time step axis.
|
|
- pres_temp_4D_wr.c
|
|
- pres_temp_4D_rd.c
|
|
|
|
Additionally, in this example the data are written and read one time
|
|
step at a time, as is typical in scientific applications that use the
|
|
unlimited dimension.
|
|
|
|
The sample data file created by pres_temp_4D_wr can be examined with
|
|
the utility ncdump (see \ref netcdf_utilities).
|
|
|
|
\code
|
|
netcdf pres_temp_4D {
|
|
dimensions:
|
|
level = 2 ;
|
|
latitude = 6 ;
|
|
longitude = 12 ;
|
|
time = UNLIMITED ; // (2 currently)
|
|
variables:
|
|
float latitude(latitude) ;
|
|
latitude:units = "degrees_north" ;
|
|
float longitude(longitude) ;
|
|
longitude:units = "degrees_east" ;
|
|
float pressure(time, level, latitude, longitude) ;
|
|
pressure:units = "hPa" ;
|
|
float temperature(time, level, latitude, longitude) ;
|
|
temperature:units = "celsius" ;
|
|
data:
|
|
|
|
latitude = 25, 30, 35, 40, 45, 50 ;
|
|
|
|
longitude = -125, -120, -115, -110, -105, -100, -95, -90, -85, -80, -75, -70 ;
|
|
|
|
pressure =
|
|
900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911,
|
|
912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923,
|
|
924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935,
|
|
936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947,
|
|
948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959,
|
|
960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971,
|
|
972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983,
|
|
984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995,
|
|
996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007,
|
|
1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019,
|
|
1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031,
|
|
1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043,
|
|
900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911,
|
|
912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923,
|
|
924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935,
|
|
936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947,
|
|
948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959,
|
|
960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971,
|
|
972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983,
|
|
984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995,
|
|
996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007,
|
|
1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019,
|
|
1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031,
|
|
1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043 ;
|
|
|
|
temperature =
|
|
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, 100, 101, 102, 103, 104,
|
|
105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
|
|
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,
|
|
129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140,
|
|
141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
|
|
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, 100, 101, 102, 103, 104,
|
|
105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
|
|
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,
|
|
129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140,
|
|
141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152 ;
|
|
}
|
|
\endcode
|
|
|
|
\section example_simple_nc4 The simple_nc4 Example
|
|
|
|
This example, like the simple_xy netCDF-3 example above, is an overly simplified example which demonstrates how to use groups in a netCDF-4 file.
|
|
|
|
This example is only available in C for this version of netCDF-4. The example creates and then reads the file “simple_nc4.nc.”
|
|
|
|
The simple_xy.nc data file contains two dimensions, “x” and “y”, two groups, “grp1” and “grp2”, and two data variables, one in each group, both named: “data.” One data variable is an unsigned 64-bit integer, the other a user-defined compound type.
|
|
|
|
The example program simple_nc4_wr.c creates the example data file simple_nc4.nc. The example program simple_nc4_rd.c reads the data file.
|
|
- simple_nc4_wr.c
|
|
- simple_nc4_rd.c
|
|
|
|
\section example_simple_xy_nc4 The simple_xy_nc4 Example
|
|
|
|
This example, like the simple_xy netCDF-3 example above, is an overly simplified example. It is based on the simple_xy example, but used data chunking, compression, and the fletcher32 filter.
|
|
|
|
(These are all HDF5 features. For more information see http://hdfgroup.org/HDF5/).
|
|
|
|
This example is not yet available in C++. We hope to have the C++ example in a future release of netCDF.
|
|
|
|
The example creates and then reads the file “simple_xy_nc4.nc.”
|
|
|
|
The example program simple_xy_nc4_wr.c creates the example data file
|
|
simple_xy_nc4.nc. The example program simple_xy_nc4_rd.c reads the
|
|
data file.
|
|
- simple_xy_nc4_wr.c
|
|
- simple_xy_nc4_rd.c
|
|
|
|
\page interoperability_hdf5 Interoperability with HDF5
|
|
|
|
NetCDF-4 allows some interoperability with HDF5.
|
|
|
|
\section reading_with_hdf5 Reading and Editing NetCDF-4 Files with HDF5
|
|
|
|
The HDF5 Files produced by netCDF-4 are perfectly respectable HDF5
|
|
files, and can be read by any HDF5 application.
|
|
|
|
NetCDF-4 relies on several new features of HDF5, including dimension
|
|
scales. The HDF5 dimension scales feature adds a bunch of attributes
|
|
to the HDF5 file to keep track of the dimension information.
|
|
|
|
It is not just wrong, but wrong-headed, to modify these attributes
|
|
except with the HDF5 dimension scale API. If you do so, then you will
|
|
deserve what you get, which will be a mess.
|
|
|
|
Additionally, netCDF stores some extra information for dimensions
|
|
without dimension scale information. (That is, a dimension without an
|
|
associated coordinate variable). So HDF5 users should not write data
|
|
to a netCDF-4 file which extends any unlimited dimension.
|
|
|
|
Also there are some types allowed in HDF5, but not allowed in netCDF-4
|
|
(for example the time type). Using any such type in a netCDF-4 file
|
|
will cause the file to become unreadable to netCDF-4. So don't do it.
|
|
|
|
NetCDF-4 ignores all HDF5 references. Can't make head nor tail of
|
|
them. Also netCDF-4 assumes a strictly hierarchical group
|
|
structure. No looping, you weirdo!
|
|
|
|
Attributes can be added (they must be one of the netCDF-4 types),
|
|
modified, or even deleted, in HDF5.
|
|
|
|
\section accessing_hdf5 Reading and Editing HDF5 Files with NetCDF-4
|
|
|
|
Assuming a HDF5 file is written in accordance with the netCDF-4 rules
|
|
(i.e. no strange types, no looping groups), and assuming that *every*
|
|
dataset has a dimension scale attached to each dimension, the netCDF-4
|
|
API can be used to read and edit the file, quite easily.
|
|
|
|
In HDF5 (version 1.8.0 and later), dimension scales are (generally) 1D
|
|
datasets, that hold dimension data. A multi-dimensional dataset can
|
|
then attach a dimension scale to any or all of its dimensions. For
|
|
example, a user might have 1D dimension scales for lat and lon, and a
|
|
2D dataset which has lat attached to the first dimension, and lon to
|
|
the second.
|
|
|
|
If dimension scales are not used, then netCDF-4 can still edit the
|
|
file, and will invent anonymous dimensions for each variable shape.
|
|
|
|
\page groups Groups
|
|
|
|
NetCDF-4 files can store attributes, variables, and dimensions in
|
|
hierarchical groups.
|
|
|
|
This allows the user to create a structure much like a Unix file
|
|
system. In netCDF, each group gets an ncid. Opening or creating a file
|
|
returns the ncid for the root group (which is named “/”). Groups can
|
|
be added with the nc_def_grp() function. Get the number of groups, and
|
|
their ncids, with the nc_inq_grps() function.
|
|
|
|
Dimensions are scoped such that they are visible to all child
|
|
groups. For example, you can define a dimension in the root group, and
|
|
use its dimension id when defining a variable in a sub-group.
|
|
|
|
Attributes defined as ::NC_GLOBAL apply to the group, not the entire
|
|
file.
|
|
|
|
The degenerate case, in which only the root group is used, corresponds
|
|
exactly with the classic data mode, before groups were introduced.
|
|
|
|
\page user_defined_types User Defined Types
|
|
|
|
\section compound_types Compound Types
|
|
|
|
In netCDF-4 files it's possible to create a data type which
|
|
corresponds to a C struct. These are known as “compound” types
|
|
(following HDF5 nomenclature).
|
|
|
|
That is, a netCDF compound type is a data structure which contains an
|
|
arbitrary collection of other data types, including other compound
|
|
types.
|
|
|
|
To define a new compound type, use nc_def_compound(). Then call
|
|
nc_insert_compound() for each type within the compound type.
|
|
|
|
Read and write arrays of compound data with the nc_get_vara() and
|
|
nc_put_vara() functions. These functions were actually part of the
|
|
netCDF-2 API, brought out of semi-retirement to handle user-defined
|
|
types in netCDF-4.
|
|
|
|
\section opaque_types Opaque Types
|
|
|
|
Store blobs of bits in opaque types. Create an opaque type with
|
|
nc_def_opaque. Read and write them with nc_get_vara()/nc_put_vara().
|
|
|
|
\section vlen_type Variable Length Arrays (VLEN)
|
|
|
|
Create a VLEN type to store variable length arrays of a known base
|
|
type. Use nc_def_vlen() to define a VLEN type, read and write them with
|
|
nc_get_vara()/nc_put_vara().
|
|
|
|
\page string_type Strings
|
|
|
|
Use the ::NC_STRING type to store arrays of strings. Read and write them
|
|
with nc_get_vara()/nc_put_vara().
|
|
|
|
\page parallel_io Parallel I/O with NetCDF-4
|
|
|
|
NetCDF-4 provides access to HDF5 parallel I/O features for
|
|
netCDF-4/HDF5 files. NetCDF classic and 64-bit offset format may not
|
|
be opened or created for use with parallel I/O. (They may be opened
|
|
and created, but parallel I/O is not available.)
|
|
|
|
A few functions have been added to the netCDF C API to handle parallel
|
|
I/O.
|
|
|
|
You must build netCDF-4 properly to take advantage of parallel
|
|
features (see \ref build_parallel).
|
|
|
|
The nc_open_par() and nc_create_par() functions are used to
|
|
create/open a netCDF file with parallel access.
|
|
|
|
The parallel access associated with these functions is not a
|
|
characteristic of the data file, but the way it was opened.
|
|
|
|
\section collective_independent Collective/Independent Access
|
|
|
|
Parallel file access is either collective (all processors must
|
|
participate) or independent (any processor may access the data without
|
|
waiting for others).
|
|
|
|
All netCDF metadata writing operations are collective. That is, all
|
|
creation of groups, types, variables, dimensions, or attributes.
|
|
|
|
Data reads and writes (ex. calls to nc_put_vara_int() and
|
|
nc_get_vara_int()) may be independent (the default) or collective. To
|
|
make writes to a variable collective, call nc_var_par_access().
|
|
|
|
\page tutorial_ncids Numbering of NetCDF IDs
|
|
|
|
In C, Fortran 77, and Fortran 90, netCDF objects are identified by an
|
|
integer: the ID. NetCDF functions use this ID to identify the
|
|
object. It's helpful for the programmer to understand these IDs.
|
|
|
|
Open data files, dimensions, variables, and attributes, and
|
|
used-defined types are each numbered independently, and are always
|
|
numbered in the order in which they were defined. (They also appear in
|
|
this order in ncdump output.) Numbering starts with 0 in C, and 1 in
|
|
Fortran 77/90.
|
|
|
|
For example, the first variable defined in a file will have an ID of 0
|
|
in C programs, and 1 in Fortran programs, and functions that apply to
|
|
a variable will need to know the ID of the variable you mean.
|
|
|
|
IDs for netCDF dimensions and variables are persistent, but deleting
|
|
an attribute changes subsequent attribute numbers.
|
|
|
|
Although netCDF refers to everything by an integer id (varid, dimid,
|
|
attnum), there are inquiry functions which, given a name, will return
|
|
an ID. For example, nc_inq_varid() will take a character
|
|
string (the name), and give back the ID of the variable of that
|
|
name. The variable ID is then used in subsequent calls (to read the
|
|
data, for example).
|
|
|
|
The ncid used to identify a file in the classic model, or a group
|
|
within that file in the enhanced model (see \ref netcdf_data_model), or a
|
|
user-defined type, are not permanently associated with the file. They
|
|
may change the next time the file is opened.
|
|
|
|
\page creating Creating New Files and Metadata, an Overview
|
|
|
|
To construct a netCDF file you need to:
|
|
- create the file - Specify the name, optionally the format: classic
|
|
(the default) or 64bit-offset.
|
|
- define metadata - Specify the names and types of dimensions, data
|
|
variables, and attributes.
|
|
- write data - Write arrays of data from program variables to the
|
|
netCDF file. Arrays of data may be written all at once, or in subsets.
|
|
- close the file - Close the file to flush all buffers to the disk and
|
|
free all resources allocated for this file.
|
|
|
|
\page reading_known Reading NetCDF Files of Known Structure
|
|
|
|
To read a netCDF file of known structure, you need to:
|
|
- open the file - Specify the file name and whether you want
|
|
read-write or read-only access.
|
|
- read variable or attribute data - Read the data or attributes of
|
|
interest.
|
|
- close the file - Release all resources associated with this file.
|
|
|
|
Use ncdump to learn the structure of a file (use the -h option).
|
|
|
|
\page reading_unknown Reading NetCDF Files of Unknown Structure
|
|
|
|
Perhaps you would like to write your software to handle more general
|
|
cases, so that you don't have to adjust your source every time the
|
|
grid size changes, or a variable is added to the file.
|
|
|
|
There are inquiry functions that let you find out everything you need
|
|
to know about a file. These functions contain “inq” or “INQ” in their
|
|
names.
|
|
|
|
Using the inquiry functions, it is possible to write code that will
|
|
read and understand any netCDF file, whatever its contents. (For
|
|
example, ncdump does just that.)
|
|
|
|
First use nc_inq(), which will tell you how many variables and global
|
|
attributes there are in the file.
|
|
|
|
Start with global attribute 0, and proceed to natts - 1, the number of
|
|
global attributes minus one. The nc_inq_att() function will tell you
|
|
the name, type, and length of each global attribute.
|
|
|
|
Then start with dimid 0, and proceed to dimid ndims - 1, calling
|
|
nc_inq_dim(). This will tell you the name and length of each
|
|
dimension, and whether it is unlimited.
|
|
|
|
Then start with varid 0, and proceed to varid nvars - 1, calling
|
|
nc_inq_var(). This will tell you the number of dimensions of this
|
|
variable, and their associated IDs. It will also get the name and type
|
|
of this variable, and whether there are any attributes attached. If
|
|
there are attributes attached, use the nc_inq_att() function to get
|
|
their names, types, and lengths.
|
|
|
|
(To read an attribute, use the appropriate nc_get_att_<TYPE> function,
|
|
like nc_get_att_int() to get the data from an attribute that is an
|
|
array of integers.)
|
|
|
|
There are also functions that return an item's ID, given its name. To
|
|
find IDs from the names, use functions nc_inq_dimid(),
|
|
nc_inq_attnum(), and nc_inq_varid().
|
|
|
|
The inquiry functions are:
|
|
- nc_inq() Find number of dimensions, variables, and global
|
|
attributes, and the unlimited dimid.
|
|
- nc_inq_att() Find attribute name, type, and length.
|
|
- nc_inq_dim() Find dimension name and length.
|
|
- nc_inq_var() Find variable name, type, num dimensions, dim IDs, and
|
|
num attributes.
|
|
- nc_inq_dimid() Find dimension ID from its name.
|
|
- nc_inq_varid() Find variable ID from its name.
|
|
- nc_inq_format() Find file format: classic or 64-bit offset
|
|
- nc_inq_libvers() Find the netCDF library version.
|
|
|
|
\page accessing_subsets Reading and Writing Subsets of Data
|
|
|
|
Usually users are interested in reading or writing subsets of
|
|
variables in a netCDF data file. The netCDF APIs provide a variety of
|
|
functions for this purpose.
|
|
|
|
In the simplest case, you will use the same type for both file and
|
|
in-memory storage, but in some cases you may wish to use different
|
|
types. For example, you might have a netCDF file that contains integer
|
|
data, and you wish to read it into floating-point storage, converting
|
|
the data as it is read. The same sort of type conversion can be done
|
|
when writing the data.
|
|
|
|
To convert to a type while reading data, use the appropriate
|
|
nc_get_vara_<TYPE> or NF_GET_VARA_<TYPE> function. For example, the C
|
|
function nc_get_vara_float(), and the Fortran function
|
|
NF_GET_VARA_REAL will read netCDF data of any numeric type into a
|
|
floating-point array, automatically converting each element to the
|
|
desired type.
|
|
|
|
To convert from a type while writing data, use the appropriate
|
|
nc_put_vara_<TYPE> or NF_PUT_VARA_<TYPE> function. For example, the C
|
|
function nc_put_vara_float() will write floating-point data into
|
|
netCDF arrays, automatically converting each element of the array to
|
|
the type of the netCDF variable.
|
|
|
|
The TYPE in the function name refers to the type of the in-memory
|
|
data, in both cases. They type of the file data is determined when the
|
|
netCDF variable is defined.
|
|
|
|
The type of the data may be automatically converted on read or
|
|
write.
|
|
|
|
\example simple_xy_wr.c
|
|
\example simple_xy_rd.c
|
|
\example sfc_pres_temp_wr.c
|
|
\example sfc_pres_temp_rd.c
|
|
\example pres_temp_4D_wr.c
|
|
\example pres_temp_4D_rd.c
|
|
\example simple_nc4_wr.c
|
|
\example simple_nc4_rd.c
|
|
\example simple_xy_nc4_wr.c
|
|
\example simple_xy_nc4_rd.c
|
|
*/
|