This document provides references to software packages that may be used for manipulating or displaying netCDF data. We include information about both freely-available and licensed (commercial) software that can be used with netCDF data. We rely on developers to help keep this list up-to-date. If you know of corrections or additions, please send them to us. Where practical, we would like to include WWW links to information about these packages in the HTML version of this document.
Other useful guides to utilities that can handle netCDF data include ARM's list of ARM-tested netCDF data tools, which includes some downloadable binaries and the NOAA Geophysical Fluid Dynamics Laboratory guide to netCDF utilities.
The ARM Program has developed ANDX (ARM NetCDF Data eXtract), a command-line utility designed for routine examination and extraction of data from netcdf files. Data can be displayed graphically (line-plot, scatter-plot, overlay, color-intensity, etc.) or extracted as ASCII data. Whether displayed graphically or extracted as ASCII, results can be saved to disk or viewed on screen.
ANAX (ARM NetCDF ASCII eXtract) is a scaled-down version of ANDX -- it is designed to only extract ASCII data. All features of ANDX pertaining to non-graphic data extraction are included in ANAX.
The ARM Program has developed ANTS (ARM NetCDF Tool Suite), a collection of netCDF tools and utilities providing various means of creating and modifying netcdf files. ANTS is based on nctools written by Chuck Denham. The utilities within nctools were modified to compile with version 3.5 of the netCDF library, the command syntax was modified for consistency with other tools, and changes were made to accommodate ARM standard netCDF.
The original functions from nctools were intended mainly for the creation, definition, and copying of fundamental netCDF elements. ARM added others which focus on manipulation of data within existing netCDF files. Additional functions have special support for multi-dimensional data such as "slicing" cross sections from multi-dimensional variable data or joining lesser-dimensional fields to form multi-dimensional structures. Functions have been added to support execution of arithmetic and logical operations, bundling or splitting netCDF files, comparing the structure or content of files, and so on.
Essentially every type of netCDF library function call is exercised in ANTS. In this way then, this open-source collection of tools also represents a library of coding examples for fundamental netCDF tasks. See the website for more information.
ARGOS (interActive thRee-dimensional Graphics ObServatory) is a new IDL-based interactive 3D visualization tool, developed by David N. Bresch and Mark A. Liniger at the Institute for Atmospheric Science at the Swiss Federal Institute of Technology, ETH, ZÃ¼rich.
A highly optimized graphical user interface allows quick and elegant creation of even complex 3D graphics (volume rendering, isosurfaces,...), including Z-buffered overlays (with hidden lines), light and data shading, Xray images, 3D trajectories, animations and virtual flights around your data, all documented in a full on-line html-help. The netCDF data format is preferred, but any other format can be read by providing an IDL (or FORTRAN or C or C++) interface. Some toolboxes (for atmospheric model output, trajectory display, radar data) have already been written, others might easily be added (in IDL, FORTRAN or C code). All interactive activities are tracked in a script, allowing quick reconstruction of anything done as well as running ARGOS in batch script mode.
Information about copyright and licensing conditions are available. For further information and installation, please E-mail to: email@example.comClimate Data Analysis Tool (CDAT), developed by the Program for Climate Model Diagnosis and Intercomparison (PCMDI) at Lawrence Livermore National Laboratory, provides the capabilities needed to analyze model data, perform complex mathematical calculations, and graphically display the results. It provides the necessary tools to diagnose, validate, and intercompare large observational and global climate model data sets.
It includes the ability to ingest large climate datasets in netCDF, HDF, DRS, and GrADS/GRIB format; the Visualization and Computation System (VCS) module, visually displays and animates ingested or created data; and the Library of AMIP Data Transmission Standards (LATS) module outputs data in the machine-independent netCDF or GrADS/GRIB file formats.
In addition, the Command Line Interface (CLI) module allows CDAT to receive argument and function input via the command line, and the Graphical User Interface (GUI) allows CDAT to receive argument and function input via a point-and-click environment.
The software, which runs as a standalone process or within PCMDI's Visualization and Computation System (VCS), provides climate scientists with an easy and fast method to read different file formats, and to analyze and graphically display climate data in an integrated fashion. CDAT includes a set of pre-defined functions to allow the user to manipulate the data and send the output to a file which can be viewed as an image, or as a collection of images in an animation. The software has a gradual learning curve, allowing the novice user to quickly obtain useful results.
The MRG CDFconvert package provided by the Mesoscale Research Group, McGill University/SUNY Albany, is designed to address data conversion issues for gridded datasets stored under the COARDS convention. CDFconvert converts regular Cylindrical Equidistant (Lat/Long) and Gaussian (Spherical) netCDF grids into either the Canadian RPN Standard File or GEMPAK file formats. MRG CDFconvert has the flexibility to handle netCDF files generated by a number of sources, including NCEP and ECMWF. User-definable conversion tables make the extension of the package to different datasets possible.
Joe Sirott of NOAA's Pacific Marine Environmental Laboratory has developed cdfsync, a program that allows users to rapidly synchronize a set of netCDF files over a network. Fast synchronization times are achieved by only transmitting the differences between files. It is built on the Open Source rsync program, but contains a number of optimizations including:
The latest version should run on Linux variants and Solaris.More information is available at the cdfsync website.
Uwe Schulzweida at the Max Planck Institute for Meteorology has developed CDO, a collection of Operators to manipulate and analyze Climate Data files. Supported file formats include netCDF and GRIB. There are more than 350 operators available. The following table provides a brief overview of the main categories.
As an example of use of CDO, converting from GRIB to netCDF can be as simple as
cdo -f nc copy file.grb file.ncor with relative time axis (for usage with GrADS)
cdo -r -f nc copy file.grb file.ncor using ECMWF reanalysis on a reduced grid
cdo -R -f nc copy file.grb file.nc
More information is available on the CDO homepage.C4) Integrated Data Systems (CIDS) group has developed several useful netCDF utilities:
The CSIRO MATLAB/netCDF interface is run from within MATLAB and has a simple syntax. It has options for automatically handling missing values, scale factors, and permutation of hyperslabs. It is, however, limited to retrieving data from, and information about, existing netCDF files.
The basis of the interface is a machine-dependent mex-file called mexcdf53. Rather than call the mex-file directly users are advised to employ both Chuck Denham's netCDF toolbox and the CSIRO MATLAB/netCDF interface described here. For read-only access to existing netCDF data, the CSIRO interface has a simpler syntax than the netCDF Toolbox, but the latter may also be used to create and manipulate netCDF variables and datasets.PMEL) has developed the EPIC software package for oceanographic data. EPIC provides graphical display and data field manipulation for multi-dimensional netCDF files (up to 4 dimensions). PMEL has been using this software on Unix and VMS several years. At present, they have:
The developers are interested in coordinating with others who may be developing oceanographic software for use with netCDF files. The EPIC software is available via anonymous FTP from ftp.noaapmel.gov in the epic/ and /eps directories. To obtain the EPIC software, please see Web pages at http://www.pmel.noaa.gov/epic/download/index.html. For information about EPIC, please see the Web pages at http://www.pmel.noaa.gov/epic/index.html. Contact firstname.lastname@example.org, or Nancy Soreide, email@example.com, for more information.
Several packages are available for accessing netCDF data from Microsoft Excel, including the netcdf4excel add-in for Excel, and a Scientific Dataset (SDS) Library that supports a DataSetEditor add-in for Excel to view and modify various forms of data, including netCDF.EzGet has been developed at PCMDI to facilitate retrieval of modeled and observed climate data stored in popular formats including DRS, netCDF, GrADS, and, if a control file is supplied, GRIB. You can specify how the data should be structured and whether it should undergo a grid transformation before you receive it, even when you know little about the original structure of the stored data (e.g., its original dimension order, grid, and domain).
The EzGet library comprises a set of subroutines that can be linked to any FORTRAN program. EzGet reads files through the cdunif interface, but use of EzGet does not require familiarity with cdunif. The main advantages of using EzGet instead of the lower level cdunif library include:
For more information about EzGet, including instructions for downloading the documentation or software, see the EzGet home page at http://www-pcmdi.llnl.gov/ktaylor/ezget/ezget.html. For questions or comments on EzGet, contact Karl Taylor (firstname.lastname@example.org).FAN (File Array Notation) is Harvey Davies' package for extracting and manipulating array data from netCDF files. The package includes the three utilities nc2text, text2nc, and ncrob for printing selected data from netCDF arrays, copying ASCII data into netCDF arrays, and performing various operations (sum, mean, max, min, product, ...) on netCDF arrays. A library (fanlib) is also included that supports the use of FAN from C programs. The package is available via anonymous FTP from ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/fan.tar.Z. Questions and comments may be sent to Harvey Davies, email@example.com. FERRET is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. It is available by anonymous ftp from abyss.pmel.noaa.gov for a number of computer systems: SUN (Solaris and SUNOS), DECstation (Ultrix and OSF/1), SGI, VAX/VMS and Macintosh (limited support), and IBM RS-6000 (soon to be released).
FERRET offers a Mathematica-like approach to analysis; new variables may be defined interactively as mathematical expressions involving data set variables. Calculations may be applied over arbitrarily shaped regions. Fully documented graphics are produced with a single command. Graphics styles included line plots, scatter plots, contour plots, color-filled contour plots, vector plots, wire frame plots, etc. Detailed controls over plot characteristics, page layout and overlays are provided. NetCDF is supported both as an input and an output format.
Many excellent software packages have been developed recently for scientific visualization. The features that make FERRET distinctive among these packages are Mathematica-like flexibility, geophysical formatting (latitude/longitude/date), "intelligent" connection to its data base, special memory management for very large calculations, and symmetrical processing in 4 dimensions. Contact Steve Hankin, firstname.lastname@example.org, for more information.
Heiko Klein (Norwegian Meteorological Institute) has developed the fimex (File Interpolation, Manipulation, and EXtraction) C++ library for gridded geospatial data. It converts between several data formats (currently netCDF, NcML, GRIB1 or GRIB2, and felt). Fimex also enables you to change the projection and interpolation of scalar and vector grids, to subset the gridded data, and to extract only parts of the files. Fimex supports a growing list of other features, including support for most NcML features and for netCDF-4 compression.
For simple usage, Fimex also comes with the command line program fimex.
Documentation and downloads are available from the fimex web site.
FWTools is Frank Warmerdam's set of Open Source GIS binaries for Windows (win32) and Linux (x86 32bit) systems. The kits are intended to be easy for end users to install and get going with, and include OpenEV, GDAL, MapServer, PROJ.4 and OGDI as well as some supporting components. FWTools aims to track the latest development versions of the packages included as opposed to official releases, "to give folks a chance to use the latest and greatest".
Frank Warmerdam's GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license. As a library, it presents a single abstract data model to the calling application for all supported formats. The related OGR library (which lives within the GDAL source tree) provides a similar capability for simple features vector data.
GDAL is in active use in several projects, and includes roughly 40 format drivers, including a translator for netCDF (read/write). Other translators include GeoTIFF (read/write), Erdas Imagine (read/write), ESRI .BIL (read), .aux labeled raw (read/write), DTED (read), SDTS DEM (read), CEOS (read), JPEG (read/write), PNG (read/write), Geosoft GXF (read) and Arc/Info Binary Grid (read). A full list is available in Supported Formats.
GDAL has recently included support for the netCDF-4 enhanced data model and netCDF-4 format, as well as improved support for recent additions to the CF conventions.
As an example of the use of GDAL, converting an ArcInfo ASCII grid to netCDF (GMT conventions) as easy as:
gdal_translate arc_ascii.grd -of GMT gmt_grid.nc
Gfdnavi is a web-based tool to archive, share, distribute, analyze, and visualize geophysical fluid data and knowledge. The software is under development by members of the GFD Dennou Club, including T. Horinouchi (RISH, Kyoto U.), S. Nishizawa (RIMS, Kyoto U.), and colleagues. Gfdnavi uses a metadata database for managing and analyzing data and visualizations. It also permits publishing data for web access and will soon support access to data on other Gfdnavi servers. Web service APIs are now under development. A presentation Introducing Gfdnavi describes the architecture and shows examples of use.
Gfdnavi is dependent on two technologies:
Dr L. Mun Woo
Being interactive, Gliderscope speaks to users via an onscreen dialogue box, helping the user decide what to do. With a few simple clicks of the mouse, users can choose and extract segments of data, filter out the bad data, perform calculations (e.g. for water density, sound velocity in water, light attenuation, 1% photic depth) and apply a variety of high level graphical data visualisation techniques to produce elegant three/four-dimensional plots of water properties, interpolated contour charts, vertical profile plots, water properties comparison charts etc. Additionally, users can also export their data to text or NetCDF files for easy access in other applications. Gliderscope is available on Windows and Macintosh platforms, as standalone executable software as well as an App for use within Matlab.
GMT (Generic Mapping Tools) is an open source collection of about 60 tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports 30 map projections and transformations and comes with support data such as coastlines, rivers, and political boundaries. GMT is developed and maintained by Paul Wessel and Walter H. F. Smith with help from a global set of volunteers, and is supported by the National Science Foundation. It is released under the GNU General Public License.
The package can access COARDS-compliant netCDF grids as well as ASCII, native binary, or user-defined formats. The GMT package is available via anonymous ftp from several servers; see gmt.soest.hawaii.edu for installation information.Grace is a tool to make two-dimensional plots of scientific data, including 1D netCDF variables. It runs under the X Window System and OSF Motif (recent versions of LessTif are, by and large, fine, too). Grace runs on practically any version of Unix. As well, it has been successfully ported to VMS, OS/2 and Win9*/NT (some functionality may be missing, though). Grace is a descendant of ACE/gr.
A few features of Grace are:
Eventually, it will be possible to integrate netCDF objects with the rest of the HDF tool suite. Such an integration will then allow tools written for netCDF and tools written for HDF to both interact intelligently with the new data files.
The Goddard Earth Sciences Data and Information Services Center (GES DISC) has developed an on-the-fly HDF-EOS to netCDF/CF converter for the following products, making them easier to use in the Unidata IDV and McIDAS-V:
Graphical output of (atmospheric model) data can be quickly generated in a large number of different ways, including horizontal maps at selected model or pressure levels, vertical north-south, east-west, or slant cross-sections (including zonal averages), time slices, animations, etc. It also allows mathematical operations on the existing fields to generate new fields for further analysis, and it can be run as a batch application.
The program handles data in netCDF, HDF and GRIB format. Interfaces to other data formats (e.g. ASCII and binary data) can be added easily.
Beginning with Version 4.0, it also supports the ability to overlay meteorological fields on a number of different satellite images, and to draw air parcel trajectories.HOPS), developed by R. Saravanan at NCAR, is a bilingual, multi-platform software package for processing data in netCDF files conforming to the NCAR-CCM format or the NCAR Ocean Model format. HOPS is implemented in IDL, the widely-used commercial interpreted language, and also in Yorick, a public-domain interpreted language that is freely available from the Lawrence Livermore National Laboratory. The IDL version of HOPS should run on any platform supported by IDL. The Yorick version too runs on most common UNIX platforms, such as Sun, SGI, Cray, and LINUX computers.
HOPS is not a monolithic program, but a suite of operators that act on data units called "hyperslabs". The design of HOPS is object-oriented, rather than procedure-oriented; the operators treat the numeric data and the associated meta-data (like coordinate information) as a single object.
Note that HOPS is not a general purpose netCDF utility and works only for the NCAR CSM netCDF formats. For more information, check the HOPS home page.
Klavs M. Sørensen, Thomas Skov and Rasmus Bro (Faculty of Life Sciences, University of Copenhagen) have developed iCDF, a free and documented toolbox for importing chromatographic data in the netCDF-based format that most manufacturers of chromatographic software support.
The iCDF software is currently for XC-MS data (X: GC, LC, HPLC), but soon it will be able to import data using other detectors as well. It can be used to open netCDF files from many different instruments (e.g. Agilent, Bruker) and many chromatographic software packages (e.g. ChemStation).
For more information, see the paper
Skov T and Bro R. (2008) Solving fundamental problems in chromatographic analysis Analytical and Bioanalytical Chemistry, 390 (1): 281-285.
Unidata's Integrated Data Viewer (IDV) is a Java application (for Java 1.4 or later) that can be used to display a variety of netCDF files, particularly well formatted, geolocated datasets. Features include:
Ingrid, by M. Benno Blumenthal <email@example.com>, is designed to manipulate large datasets and model input/output. It can read data from its data catalog, a netCDF file, or a directly attached model, and output the data, either by feeding it to a model, creating a netCDF file, or creating plots and other representations of the data.
Ingrid has a number of filters which allow simple data manipulations, such as adding two datasets together, smoothing, averaging, and regridding to a new coordinate. In addition to netCDF, it also reads HDF, CDF, VOGL, and SGI GL.
Ingrid is currently running as a WWW daemon that can be accessed through http://rainbow.ldgo.columbia.edu/datacatalog.html to see some of its capabilities on a climate data catalog maintained by the Climate Group of the Lamont-Doherty Earth Observatory of Columbia University. To quote the introduction:
The Data Catalog is both a catalog and a library of datasets, i.e. it both helps you figure out which data you want, and helps you work with the data. The interface allows you to make plots, tables, and files from any dataset, its subsets, or processed versions thereof.
This data server is designed to make data accessible to people using WWW clients (viewers) and to serve as a data resource for WWW documents. Since most documents cannot use raw data, the server is able to deliver the data in a variety of ways: as data files (netCDF and HDF), as tables (html), and in a variety of plots (line, contour, color, vector) and plot formats (PostScript and gif). Processing of the data, particularly averaging, can be requested as well.
The Data Viewer in particular demonstrates the power of the Ingrid daemon.
Ingrid currently runs on Linux, for which binaries are available. CVS access to the current source can be arranged.
The Intel® Array Visualizer and Intel® Array Viewer are available as free downloads for Windows platforms. They offer an application and a set of software tools and components, which include C, Fortran, and .Net libraries, for developing scientific visualization applications and for creating interactive graphs of array data in various formats, including HDF and netCDF.
IVE (Interactive Visualization Environment) is a software package designed to interactively display and analyze gridded data. IVE assumes the data to be displayed are contained in one- two-, three- or four-dimensional arrays. By default, the numbers within these arrays are assumed to represent grid point values of some field variable (such as pressure) on a rectangular evenly spaced grid. IVE is, nevertheless, capable of displaying data on arbitrary curvilinear grids.
If the data points are not evenly spaced on a rectangular grid, IVE must be informed of the grid structure, either by specifying "attributes" in the data input or by specifying the coordinate transform in a user supplied subroutine. Stretched rectangular grids (which occur when the stretching along a given coordinate is a function only of the value of that coordinate) can be accommodated by specifying one-dimensional arrays containing the grid-point locations along the stretched coordinate as part of the IVE input data. Staggered meshes can also be accommodated by setting "attributes" in the input data. The structure of more complicated curvilinear grids must be communicated to IVE via user supplied "transforms," which define the mapping between physical space and the array indices.
Since four-dimensional data cannot be directly displayed on a flat computer screen, it is necessary to reduced the dimensionality of the data before it is displayed. One of IVE's primary capabilities involves dimension reduction or "data slicing." IVE allows the user to display lower-dimensional subsets of the data by fixing a coordinate or by averaging over the coordinate.
IVE currently has the capability to display
IVE lets you overlay plots, loop plots, and control a wide variety of display parameters.
IVE also can perform algebraic computations on the gridded data and can calculate derivatives. More complicated computations can be performed in user supplied subroutines.
IVE uses NetCDF for the data input format, and uses the NCAR Graphics Library to produce graphical output. IVE is available as source via anonymous ftp; and as binary on request for licensees of NCAR graphics.
The program and source are available from https://github.com/jllodra/ncdump-json .
The NetCDF-Java 4.2 Library is a Java interface to netCDF files, as well as to many other types of scientific data formats. It is freely available and the source code is released under the (MIT-style) netCDF C library license. Previous versions use the GNU Lesser General Public License (LGPL).
The library implements a Common Data Model (CDM), a generalization of the netCDF, OpenDAP and HDF5 data models. The library is a prototype for the netCDF-4 project, which provides a C language API for the "data access layer" of the CDM, on top of the HDF5 file format. The NetCDF-Java library is a 100% Java framework for reading netCDF and other file formats into the CDM, as well as writing to the netCDF-3 file format. The library also implements NcML, which allows you to add metadata to CDM datasets, as well as to create virtual datasets through aggregation.
Kst is an open-source, cross-platform 2D plotting tool focused on performance and ease of use. Packages for Windows, various Linux distributions and Mac OS X are available, as well as the complete source code and CMake-based build files. A more detailed presentation of Kst can be found on the web page at http://kst-plot.kde.org, including numerous screenshots and all the useful download links.
Kst is characterized by the following features:
A netCDF Labview interface, implemented in the Labview programming language is available. The software includes A graphical user interface for editing netCDF data and conversion to other data formats. The package was developed and is maintained by L. F. Hwang of Sun Yat-sen University in China. For more information and to download the source code, see the NetCDFLabview web site.
MBDyn is an open-source MultiBody Dynamics analysis system developed at the Dipartimento di Ingegneria Aerospaziale of the University "Politecnico di Milano", Italy. It uses netCDF as its primary output format.
MBDyn features the integrated multidisciplinary analysis of multibody, multiphysics systems, including nonlinear mechanics of rigid and flexible constrained bodies, smart materials, electric networks, active control, hydraulic networks, essential fixed-wing and rotorcraft aerodynamics. It allows users to simulate the behavior of heterogeneous mechanical, aero-servo-elastic systems based on first principles equations. It is being actively developed and used in the aerospace and automotive fields for dynamics analysis and simulation of complex systems. Dynamic linking of user-defined modules is heavily exploited to let users extend the feature library.
This is a program which compares two NetCDF files. Variables with the same ID in the two files are assumed to be of the same type and have the same shape. For each such couple of variables, the program computes the maximum of the absolute value of the difference, and the maximum of the absolute value of the relative difference. The program also tells you at what location (the subscript list of the array) the maximum difference is reached.
The web page for this program is: max_diff_nc
This is a freely available tool.
MeteoExplorer, developed by Lianqing Yu at China Meteorological Administration, is a cross-platform software application for analyzing and rendering atmospheric science and geoscience data. It supports popular data formats including WMO GRIB1/GRIB2, NetCDF, and MICAPS, and provides basic GIS functionalities. Developed with C++, Meteo Explorer targets multiple computing platforms including Microsoft Windows, GNU Linux, and SGI IRIX operating systems.
The primary features include:
For more information, please visit MeteoExplorer's home page or contact the support staff via firstname.lastname@example.org .
For better cross-platform support, MeteoInfo has recently been re-developed using Unidata's NetCDF Java library. MeteoInfo is GIS software for visualization and analysis of spatial and meteorological data. The Java edition can be run in Windows, Mac OS, Linux, and Unix systems. The Groovy script engine was coupled in the software, so users can write Groovy script to run the software automatically for analysis with complex steps.
Java 6 is needed to run the software.PMEL has developed a MATLAB interface, MexEPS, which supports several netCDF file conventions, including those adopted by PMEL. Many styles of time axes are supported and time manipulation routines ease the use of the time axis in MATLAB. The MexEPS package supports the following data formats:
The MexEPS package is freely available in PMEL's anonymous ftp directory ftp://ftp.pmel.noaa.gov/eps/mexeps/
If you have any questions or comments, please contact the author, Willa Zhu (email@example.com) or Nancy Soreide (firstname.lastname@example.org).
John Evans of Rutgers University maintains MEXNC and developed SNCTOOLS. MEXNC is a mexfile interface to NetCDF files for MATLAB that has roughly a one-to-one equivalence with the C API for netCDF. SNCTOOLS is a set of higher-level m-files that sit atop MEXNC, shielding the user from such low level netCDF details as file IDs, variable IDs, and dimension IDs. The general philosophy behind SNCTOOLS is providing the ability to read and write data without trying to invent a new syntax.
Joaquim Luis of Universidade do Algarve has developed Mirone, a Windows MATLAB-based framework tool that allows the display and manipulation of a large number of grid/images formats through its interface with the GDAL library. Its main purpose is to provide users with an easy-to-use graphical interface to manipulate GMT grids. In addition it offers a wide range of tools dedicated to topics in the earth sciences, including tools for multibeam mission planning, elastic deformation studies, tsunami propagation modeling, earth magnetic field computations and magnetic Parker inversions, Euler rotations and poles computations, plate tectonic reconstructions, and seismicity and focal mechanism plotting. The high quality mapping and cartographic capabilities for which GMT is renowned is guaranteed through Mirone's ability to automatically generate GMT cshell scripts and dos batch files.
Although Mirone is written in MATLAB, a stand-alone version to run under Windows is also provided. Regrettably this version is not as efficient as the native MATLAB code but provides a solution for users that don't have MATLAB.
J. F. Luis. Mirone: A multi-purpose tool for exploring grid data. Computers & Geosciences, 33, 31-41, 2007.
Donald Denbo of NOAA's Pacific Marine Environmental Laboratory has developed and made available ncBrowse, a Java application (JDK1.2) that provides flexible, interactive graphical displays of data and attributes from a wide range of netCDF data file conventions. Features include:
ncBrowse will run on any UNIX or Windows machine with a Java 2 (JDK1.2) virtual machine installed. Automated installation scripts are available for Windows and UNIX. Additional information on ncBrowse and download instructions are available at http://www.epic.noaa.gov/java/ncBrowse.
Questions and suggestions should be directed to <email@example.com>. If you have problems reading a netCDF file with ncBrowse, please send him a copy of the file and he'll get ncBrowse to read it!
Remik Ziemlinski of the NOAA Geophysical Fluid Dynamics Laboratory has developed nccmp, a tool to compare two netCDF files. It can use MPI, include/exclude specific variables or metadata and operates quickly. Highly recommended for regression testing with large datasets. See the Web site http://nccmp.sourceforge.net/ for more information.
The NCAR Command Language (NCL) is an interpreted programming language for scientific data analysis and visualization developed and maintained in NCAR's Computational and Information Systems Laboratory.
NCL has many features common to modern programming languages, including types, variables, operators, expressions, conditional statements, loops, and functions and procedures. NCL also has features that are not found in other programming languages, including those that handle the manipulation of metadata, the configuration of visualizations, the import of data from a variety of data formats, and an algebra that supports array operations.
NCL has robust file input and output capabilities. It allows different datasets of different formats (netCDF, netCDF-4 classic, HDF4, HDF4-EOS, GRIB-1, and GRIB-2) to be imported into one uniform and consistent data manipulation environment, which internally is the netCDF data format. NCL doesn't place any restrictions or conventions on the organization of input netCDF files.
NCL comes with many useful built-in functions and procedures for processing and manipulating data. There are over 600 functions and procedures that include routines for use specifically with climate and model data, empirical orthogonal functions, Fourier coefficients, wavelets, singular value decomposition, 1-, 2-, and 3-dimensional interpolation, approximation, and regridding, and computer analysis of scalar and vector global geophysical quantities.
The visualizations are publication-quality and highly customizable, with hundreds of options available for tweaking the looks of your graphics. NCL can generate contours, XY plots, vectors, streamlines, and can overlay these plots on many different map projections. There are also specialized functions for generating histograms, wind roses, meteograms, skew-T plots, weather maps.
Included with the software are two command line tools: "ncl_convert2nc" for converting GRIB-1/2 or HDF files to netCDF files, and "ncl_filedump" which will dump the contents of a file format that NCL recognizes (netCDF, GRIB-1/2, HDF, etc).
NCL is available under an open source license or in binary form for several popular UNIX platforms, including (but not limited to) Linux, MacOSX, and Windows/Cygwin.
Documentation and additional information on NCL are available from the NCL website, which contains hundreds of application examples for one to download. You can also contact Mary Haley, at firstname.lastname@example.org for more information.NCO (netCDF operators) is a package of command line operators that work on generic netCDF or HDF4 files:
All operators may now be OPeNDAP clients. OPeNDAP enables network transparent data access to any OPeNDAP server. Thus OPeNDAP-enabled NCO can operate on remote files accessible through any OPeNDAP server without transferring the files. Only the required data (e.g., the variable or hyperslab specified) are transferred.
The source code is freely available from the NCO home page, as is the NCO User's Guide.
For more information, contact the author, Charlie Zender.
Patrick Jöckel of the Max Planck Institute for Chemistry has developed ncregrid, a tool (written in FORTRAN-90) for data transfer of gridded 2- and 3-dimensional (spatial) geophysical/geochemical scalar fields between grids of different resolutions. The algorithm handles data on rectangular latitude/longitude grids (not necessarily evenly spaced) and vertical pressure hybrid grids of arbitrary resolution. The input/output data format is netCDF. ncregrid is freely available without any warranty under the GNU public license (GPL). ncregrid can be used as a "stand-alone" program, and/or linked as an interface to a model, in order to re-grid automatically the input from an arbitrary grid space onto the required grid resolution.
More information is available on the web-page: http://www.mpch-mainz.mpg.de/~joeckel/ncregrid/index.html.
nctoolbox is a MATLAB interface that provides read-only access to Common Data Model datasets. Under the hood, nctoolbox uses Unidata's NetCDF-Java as the data access layer. This allows nctoolbox to access to netCDF, OPeNDAP, HDF5, GRIB, GRIB2, HDF4, and many (15+) other file formats and services using the same API. It works with MATLAB 2008a and later. The nctoolbox software was developed by Brian Schlining (MBARI), Rich Signell (USGS), Sachin Kumar Bhate (freelance), and Alex Crosby (RPS/ASA).
Patrick Jöckel of the Max Planck Institute for Chemistry has developed ncdx, a tool (written in FORTRAN-90) that scans a netCDF file and makes it OpenDX compliant. ncdx is freely available without any warranty under the GNU public license (GPL). More information is available on the web-page: http://www.mpch-mainz.mpg.de/~joeckel/ncdx/index.html.
Alan Iwi, of Rutherford Appleton Laboratory, offers this command line ensemble statistics utility. More information is available on the web-page: http://home.badc.rl.ac.uk/iwi/ncensemble/.Ncview is a visual browser for netCDF files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher. For more information, check out the README file; you can also see a representative screen image (GIF, 66K) of ncview in action. NetCDF Toolbox for MATLAB-5, originally developed by Charles R. Denham, combined netCDF-3 with MATLAB to form an interface that used MATLAB operator-syntax for arithmetic, logical, and subscripting operations on netCDF entities. The NetCDF Toolbox is in bug-fix-only mode, and is maintained by John.G.Evans.NE@gmail.com, on the MEXNC, SNCTOOLS, and the NetCDF Toolbox web page.
Ncvtk was designed from the ground up with the aim of offering a high degree of interactivity to scientists who have a need to explore structured, three-dimensional, time-dependent climate data on the sphere. A graphical user interface allows users to interact with their data via color/transparency/contour/vector plots, apply vertical slices, probe data, apply an external sun light, overlay hydrographic and geopolitical data, rotate, zoom, etc. with minimal fuss.
Ncvtk is written in python and is based on the Visualization Toolkit (VTK). Like python and VTK, Ncvtk is highly portable and known to run on Windows and Linux (i386, ia64, EMT64) platforms. More information about Ncvtk is available at http://ncvtk.sourceforge.net.
Dr L. Mun Woo of University of Western Australia
The NetCDF tools is a free software package consisting of a few tools operating on NetCDF and, by utilizing the compatibility API, HDF4 files, which are intended to be usable from Shell scripts.
The currently packaged tools are:
The ncget tool implements functionalilty that is similar to hdp dumpsds (for NetCDF, which lacks such a tool), or complements it in the case of HDF4. It can be seen as a complement to the ncdump tool (included in both the NetCDF and HDF4 distributions) as well.
This tool allows a selected part of a NetCDF variable or an HDF4 scientific data set (SDS) to be extracted in either an ASCII or binary form, applying the transformation specified by the usual scale_factor and add_offset attributes. It allows one to feed the data contained in NetCDF variables (or HDF4 SDS) to the tools designed to operate on either ASCII (text) or raw (binary) data.
This version of the package is the first one to be announced to the public. It has some known bugs and limitations, but it's proved to be quite usable. A project page on freshmeat.net. The source is also available.
For developers, the open-source (GPL V3 license) can be downloaded directly or checked out with Mercurial.
The add-in is written in VBA 6.0 (so it won't work with Office 2010 64 bits) and is designed for Excel 2007 running with the Microsoft Windows operating system. It supports opening netCDF classic format data with Excel for read or write access.
More details are available on the netcdf4excel web site.
Lionel Guez has developed and made feely available NetCDF95, a new alternative Fortran interface to the NetCDF library. Compared to the Unidata-provided Fortran 90 netCDF interface, the NetCDF95 interface is meant to be easier to use and more secure.
Tom Moore has an Objective-C API, available here: www.paleoterra.com/software. The netCDF Framework is an open source (Argonne Open Source License) MacOSX application framework that provides an Objective-C interface to the NCAR netCDF library version 3. The framework is available both as source code and universal compiles (works on both PPC and Intel macs). The source code has also been compiled by users for the GNUStep environment. Version 2 of the framework will provide classes for accessing multiple netCDF files, working with in-memory data slabs using standard notation, and some support for multithreading.
Mark Tracy has written NetcdfStep, an Objective-C API for netCDF that uses Objective-C Foundation Classes.
NetcdfStep is framework for using the netCDF library in object-oriented programming with Objective-C. It now supports the full functionality of netCDF 3.6.2.
A complete Mac OS X distribution including pre-built static library and online documentation are available. Applications linked to this framework have no external dependencies (other than Mac OS X itself). A source-code only distribution synced up to version 0.6.1 is available for GNUstep for use on Linux and other Unix platforms.
The ARM Program has contributed NCMEX for Octave, a port of Chuck Denham's MATLAB NCMEX to Octave. The calling syntax is identical, so scripts using NCMEX in MATLAB should in theory be portable to Octave. In order to build NCMEX, a compiled C NetCDF library must already be installed.
In addition to the base NetCDF library interface, this package includes a simple toolbox to automate the reading and writing of NetCDf files within Octave using NCMEX. These tools as well as the source for NCMEX are available from http://engineering.arm.gov/~sbeus/octavex/octavex.tar (NOTE: this .tar file contains other Octave extension functions besides NCMEX.)
Also see Octcdf, a netCDF toolbox for Octave.
For installation instructions, see the README file inside the .tar file.
Alexander Barth has contributed the following:
Octcdf is a netCDF toolbox for Octave which uses the same operator syntax as the matlab netCDF toolbox of Charles R. Denham. NetCDF dimensions, attributes and variables are Octave objects and can be accessed, sliced and changed just as regular variables. Unlike most netCDF toolboxes for matlab, it does not depend on the NCMEX wrapper around the netCDF interface. This octave toolbox is written in C++ calling directly the netCDF library. The octcdf toolbox can also be used to download data from an OpenDAP server. The octcdf source code is available at http://modb.oce.ulg.ac.be/mediawiki/index.php/NetCDF_toolbox_for_Octave. It was also included in the Octave Repository octave-forge.
The OPeNDAP (formerly known as DODS) is an Open-source Project for a Network Data Access Protocol that makes local data and subsets of local data accessible to remote locations independent of the local storage format. OPeNDAP also provides tools for transforming existing applications into OPeNDAP clients, enabling them to remotely access OPeNDAP served data. OPeNDAP is based on existing data access tools; rather than developing a self contained system, it makes extensive use of existing data access APIs.
OPeNDAP can be used to make netCDF data files available over the Internet and it can also be used to adapt existing software which use the netCDF API (by re-linking) to read data served by an OPeNDAP data server. In principle, any program written using netCDF can be adapted to read data from an OPeNDAP server - in other words any program which uses netCDF can become a client in the OPeNDAP client-server system. Included in the source and binary distributions are two freely available programs that have already been modified (re-linked).
With a client program accessing data from a netCDF server, it is possible to access a small subset of a large dataset over the Internet without copying the entire dataset (as you would have to do with FTP or AFS). The client can see changes to the netCDF dataset, e.g. when new records are added (which would not be possible with FTP). Finally, the client can also access cross-sections of variable data without paging large amounts of data across the network (as you would have to do with NFS, for example).
OPeNDAP software is freely available in both source form or binary form for selected platforms.OpenDX (formerly IBM Data Explorer, also known as simply DX) is a general-purpose software package for data visualization and analysis. It employs a data-flow driven client-server execution model and provides a graphical program editor that allows the user to create a visualization using a point and click interface.
DX runs on 7 major UNIX platforms as well as Windows 95/NT and is designed to take full advantage of multi-processor systems from IBM, SGI and Sun.
DX is built upon an internal data model, which describes and provides uniform access services for any data brought into, generated by, or exported from the software. This data model supports a number of different classes of scientific data, which can be described by their shape (size and number of dimensions), rank (e.g., scalar, vector, tensor), type (float, integer, byte, etc. or real, complex, quaternion), where the data are located in space (positions), how the locations are related to each other (connections), aggregates or groups (e.g., hierarchies, series, composites, multizone grids, etc.). It also supports those entities required for graphics and imaging operations within the context of Data Explorer. Regular and irregular, deformed or curvilinear, structured and unstructured data as well as "missing" or invalid data are supported.
The details of the data model are hidden at the user level. As a result DX operations or modules are polymorphic and appear typeless. The DX Import module, which reads data for use within Data Explorer directly utilizes data in netCDF as well as other formats (e.g., HDF, CDF). One or more variables may be selected as well as step(s) of a time series. Data in conventional netCDFs are directly imported. Since the DX data model is more comprehensive than the netCDF data model, a methodology to extend netCDF via attribute conventions (e.g., for unstructured meshes, non-scalar data and hierarchies) for use with Data Explorer is available.
DX supports a number of realization techniques for generating renderable geometry from data. These include color and opacity mapping (e.g., for surface and volume rendering), contours and isosurfaces, histograms, two-dimensional and three-dimensional plotting, surface deformation, etc. for scalar data. For vector data, arrow plots, streamlines, streaklines, etc. are provided. Realizations may be annotated with ribbons, tubes, axes, glyphs, text and display of data locations, meshes and boundaries. Data probing, picking, arbitrary surface and volume sampling, and arbitrary cutting/mapping planes are supported.
DX supports a number of non-graphical functions such as point-wise mathematical expressions (e.g., arithmetic, transcendental, boolean, type conversion, etc.), univariate statistics and image processing (e.g., transformation, filter, warp, edge detection, convolution, equalization, blending, morphological operations, etc.). Field/vector operations such as divergence, gradient and curl, dot and cross products, etc. are provided. Non-gridded or scattered data may be interpolated to an arbitrary grid or triangulated, depending on the analysis requirements. The length, area or volume of various geometries may also be computed. Tools for data manipulation such as removal of data points, subsetting by position, sub/supersampling, grid construction, mapping, interpolation, regridding, transposition, etc. are available.
Tools for doing cartographic projections and registration as well as earth, space and environmental sciences examples are available at Cornell University via info.tc.cornell.edu. Also see the ncdx tool for making netCDF files OpenDX compliant.
Panoply is an application that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets. Features include:
Panoply requires that your computer have a Java SE 6 runtime environment, or better, installed.
Panoply is developed at the NASA Goddard Institute for Space Studies. Questions and suggestions should be directed to Dr. Robert B. Schmunk.
A group of researchers at Northwestern University and Argonne National Laboratory (Jianwei Li, Wei-keng Liao, Alok Choudhary, Robert Ross, Rajeev Thakur, William Gropp, and Rob Latham) have designed and implemented a new parallel interface for writing and reading netCDF data, tailored for use on high performance platforms with parallel I/O. The implementation builds on the MPI-IO interface, providing portability to most platforms in use and allowing users to leverage the many optimizations built into MPI-IO implementations. Testing so far has been on Linux platforms with ROMIO and IBM SP machines using IBM's MPI.
Documentation and code for PnetCDF is now available for testing. Although a few interfaces are not implemented yet, the current implementation is complete enough to provide significant I/O performance improvements on parallel platforms, as described in a technical report. Users are invited to test PnetCDF in their applications.
ParaView is an application designed with the need to visualize large data sets in mind. The goals of the ParaView project include the following:
ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Linux and various Unix workstations and clusters. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using a unique blend of Tcl/Tk and C++.
A vtk/ParaView reader for netCDF files can be found here.
Currently supported 3D visualizations are the following:
3D data volumes may be sliced in the X, Y, or Z plane using an interactive cutting plane. A cross section of the data volume can be viewed in a 2D window as a 2D contour plot, a vector plot, a raster image or a combination of these options superimposed. Map outlines can be used as a background for 2D cross section plots of geographic data. All data is projected according to the coordinates specified by the user for the cross section window.
The user interface provides direct manipulation tools for specifying the eye position, center of view, light sources, and color ramps. Subsetting of data can be done easily by selecting the data by index or geographic coordinate. On-line contextual help provides easy access to more detail about the software. Tutorials which range from very simple visualizations to complex combinations of data sets provide the user with a quick learning tool.
Currently PolyPaint+ accepts only data which is in the NetCDF file format. A file conversion utility which converts from raw binary data to netCDf is a part of the application.
PolyPaint+ is a joint effort of the University of Colorado and NCAR (National Center for Atmospheric Research) funded by the NASA AISRP program. A beta version of PolyPaint+ is currently available free of charge using FTP or for a nominal fee which would cover tape distribution. A license agreement must be signed in order to use it.
You may order by...
Margi Klemp University of Colorado / LASP 1234 Innovation Dr. Boulder, CO 80303 USA
The P9E Team at NASA JPL has developed Pomegranate, a python application that "webifies" science data files. Supported formats include netCDF, HDF4, HDF5, GRIB and FITS.
Pomegranate can be installed on web servers as either a WSGI or CGI application to provide webification (w10n) services. To learn more about w10n of science data files, please visit http://webification.org/. A brief help document describes how to use the demo directory to browse or download metadata or data in netCDF, JSON, or other formats by clicking on data folder and document icons.
Pomegranate can also be used as a standalone library or command line application. This greatly simplifies the retrieval of metadata and data from files in supported formats.
Pomegranate is open source software and can be downloaded from http://www.openchannelsoftware.com/projects/Pomegranate/.
NCAR's Computational and Information Systems Laboratory has developed PyNGL, a python package for scientific visualization and data analysis and PyNIO, a Python package supporting access to a variety of data formats using an interface modelled on netCDF.
Python is an interpreted, object-oriented language that is supported on a wide range of hardware and operating systems. Python information and sources can be obtained from http://www.python.org/. There are now several netCDF interfaces for Python.
Jeff Whitaker of the NOAA Earth System Research Lab has developed a netCDF-4 module for python: http://code.google.com/p/netcdf4-python/. Most new features of netCDF-4 are implemented, such as multiple unlimited dimensions, groups and zlib data compression. All the new numeric data types (such as 64-bit and unsigned integer types) are implemented. Compound and variable length (vlen) data types are supported, but the enum and opaque data types are not. Mixtures of compound and vlen data types (compound types containing vlens, and vlens containing compound types) are not supported.
xray is a higher-level interface that uses netcdf4-python internally to implement a pandas-like package for N-D labelled arrays for scientific data.
André Gosselin of the Institut Maurice-Lamontagne, Péches & Océans Canada, has implemented pycdf, a new Python interface to the netCDF library. It is available from http://pysclint.sourceforge.net/pycdf/, where you will find the install files, installation instructions, extensive documentation in text and html format, and examples. pycdf requires the Numeric python package, and installs through the simple "python setyp.py install" command.
Bill Noon (email@example.com) has implemented another netCDF Python module that allows easy creation, access, and browsing of netCDF data. The bindings also use the udunits library to do unit conversions. More information and source for Noon's Python netCDF module are available from http://snow.cit.cornell.edu/noon/ncmodule.html.
The package from Konrad Hinsen has been integrated into his ScientificPython package.
Dave Brown of NCAR's Computational and Information Systems Laboratory has developed PyNIO, a Python package that allows read and/or write access to a variety of data formats using an interface modelled on netCDF. Currently supported formats include netCDF, HDF4, GRIB1 and GRIB2 (read only), and HDF-EOS 2 Grid and Swath data (read only).
Vicente Galiano of Miguel Hernandez University has developed a Python interface to PnetCDF. This Python's package called "PyPnetCDF" allows access to NetCDF files using MPI and the library PnetCDF developed by https://parallel-netcdf.github.io. The tools are very similar to Konrad Hinsen's NetCDF package to Python but can read and write in a parallel way. For more information, see: http://www.pyacts.org/pypnetcdf.
Pupynere (PUre PYthon NEtcdf REader) Roberto De Almeida has developed pupynere, a PUre PYthon NEtcdf REader that allows read-access to netCDF files using the same syntax as the Scientific.IO.NetCDF Python module. Even though it's written in Python, the module is up to 40% faster than Scientific.IO.NetCDF and pynetcdf.
The R Project for Statistical Computing has developed R, a language and environment for statistical computing and graphics. It provides a wide variety of statistical and graphical techniques, including linear and nonlinear modelling, statistical tests, time series analysis, classification, and clustering.
David Pierce has contributed the ncdf4 package for reading netCDF data into R and for creating new netCDF dimensions, variables, and files, or manipulating existing netCDF files from R.
Pavel Michna has contributed another package, RNetCDF, that also provides access to netCDF data and to udunits calendar functions from R.
Robert Hijmans (with additional contributors) has created the R raster package for geographic data analysis and modeling. The raster package can be used for reading, writing, manipulating, analyzing and modeling gridded spatial data. The package is especially useful for large datasets that don't fit into memory, because data is processed in chunks. See Introduction to the 'raster' package for more information.
Quantum GIS (QGIS) is an Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, and Windows and supports numerous vector, raster, and database formats and functionalities. QGIS supports a desktop, browser, server, and client for viewing, editing, analysis, serving, and accessing data. Its server complies with the OGC WMS 1.3 standard. In addition to PostGIS and SpatiaLite formats, it can access data in vector formats supported by the OGR library as well as most raster formats supported by the GDAL library, including netCDF. For a more detailed list of features of the QGIS desktop, browser, server, and client, see the QGIS features page.
A group at the Research Institute for Sustainable Humanosphere (RISH) of Kyoto University has developed a netCDF interface for Ruby, an interpreted, object-oriented scripting language. This interface is intended to cover all the functionality of the C library for netCDF. Also available are combination functions such as iterators (which offer abstract ways to scan files and variables). Numeric arrays are handled by the "NArray" multi-dimensional array class, which is becoming the de facto standard multi-dimensional array for Ruby. See also the Ruby-based GPhys software and Gfdnavi tool for accessing GRIB, GrADS, and netCDF data uniformly.
More information about Ruby is available from the Ruby web site.
The Scientific DataSet Library and Tools project, developed jointly by Microsoft Research Cambridge and Moscow State University, is aimed at manipulation and visualization of multidimensional data sets.
Scientific DataSet (or SDS in short) is a .NET class library for manipulating scientific data and their metadata. SDS provides a unified API for convenient access to various data storages. Three types of storages are supported by the first release: NetCDF files, CSV text files and volatile in-memory datasets. SDS uses native NetCDF library built from version 4.0.1 both for 32 and 64-bit Windows platforms. New storage types can be added to SDS infractructure as plugins. Support for accessing TIFF image files from SDS as 2D arrays will be available soon as a separate CodePlex project.
Three applications are built on top of SDS:
You can read the Getting Started document at http://sds.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=127282 for a more detailed introduction to the Scientific DataSet software. A Windows Installation package for SDS binaries along with DataSet Viewer and DataSet Editor are available also. You can also build core class libraries and the sds utility under Mono. You may use, copy, and reproduce this software for any non-commercial purpose. For further details see license at http://sds.codeplex.com/license.
The SDS project is in beta phase and keeps evolving. You are welcome to join discussions or report issues at the CodePlex site: http://sds.codeplex.com.
Apache Spatial Information System (SIS) is a Java library for developing geospatial applications. SIS enables representation of coordinates for searching, data clustering, archiving, or any other relevant spatial needs. The library is an implementation of GeoAPI 3.0 interfaces and can be used for desktop or server applications.
SIS provides data structures for geographic data and associated metadata along with methods to manipulate those data structures. The SIS metadata module forms the base of the library and enables the creation of metadata objects which comply with the ISO 19115 metadata model and which can be read from or written to ISO 19139 compliant XML documents. The SIS referencing module will enable the construction of geodetic data structures for geospatial referencing based on the ISO 19111 model such as axis, projection and coordinate reference system definitions, along with the associated operations which enable the mathematical conversion of coordinates between different systems of reference. The SIS storage modules will provide a common approach to the reading and writing of grid coverages applicable to simple imagery and multidimensional data structures.
SIS supports creating ISO 19115 metadata from metadata in a netCDF store from a given file, URL, stream, or NetcdfFile object. SIS netCDF storage is intended to be a bridge between NetCDF Climate and Forecast (CF) conventions and ISO 19115 metadata.
SIS is under development as an Apache project. Release 0.3 is currently available for download.
Dan Schmitt has developed cdftcl, a Tcl/Tk interface for netCDF. It allows the use of "wildcards" (*) or ranges (1-4) in the subscript notation, and use of name references instead of variable IDs. Contact firstname.lastname@example.org for more information.
Tcl-nap (n-dimensional array processor) is a loadable extension of Tcl which provides a powerful and efficient facility for processing data in the form of n-dimensional arrays. It has been designed to provide an array-processing facility with much of the functionality of languages such as APL, Fortran-90, IDL, J, matlab, and octave.
Support is provided for data based on n-dimensional grids, where the dimensions correspond to continuous spatial coordinates. There are interfaces to the HDF and netCDF file formats commonly used for such data, especially in Earth sciences such as Oceanography and Meteorology.
The internal data structure is called a NAO (n-dimensional array object) and contains similar information to that of HDF SDSs and netCDF variables.
Tcl-nap was developed as part of the CSIRO CAPS project, but can be loaded and used without the (satellite oriented) CAPS extension.
Carsten Wieczorrek has developed code in VB 6 to export chromatographic data into the netcdf/ANDI format. The application writes netCDF files that can be read by CHROMELEON, for example. For others interested in programming with netcdf.dll from VB 6, see Wieczorrek's web page on netCDF and VB 6.0 and for VB.net, see netCDF and VB.net.VisAD is a Java class library for interactive and collaborative visualization and analysis of numerical data. It combines:
NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA's National Centers for Environmental Information (NCEI). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. The WCT also provides access to weather/climate web services provided from NCEI and other organizations.
The WCT provides tools for background maps, animations and basic filtering. The export of images and movies is provided in multiple formats. The data export feature supports conversion of data to a variety of common formats including GeoJSON, KMZ, Shapefile, Well-Known Text, GeoTIFF, ESRI Grid and Gridded NetCDF. These data export features promote the interoperability of weather and climate information with various scientific communities and common software packages such as ArcGIS, Google Earth, MatLAB, QGIS, R and many more. Advanced data export support for Google Earth enables the 2-D and 3D export of rendered data and isosurfaces.
WebWinds is a free Java-based science visualization and analysis package. In addition to several new analysis tools, the current fourth version does automatic scripting. This allows
This scripting requires no knowledge of the scripting language syntax. Several sample script files are included with the distribution.
In addition, this version contains a capability to geo-reference some data and to read ASCII data in tabular format. Also new is the ability to output data in numerical form (e.g. NetCDF) and a context sensitive, integrated help system.
As with earlier versions, data in several different formats, including NetCDF, can be read in easily from your local machine or from the Web. In addition, most data can be subset or subsampled on load, making it possible to visualize very large multidimensional and/or multispectral datasets. The package includes several step-by-step examples. Installation of the software (including Java) on the PC or Mac is a process requiring one file to be downloaded and opened. If you need help getting started, a remote tutorial is available once you've downloaded the package.
WebWinds is `point and click' rather than language driven and it runs well on Unix, Windows (95/98/NT) and Mac platforms. It currently requires JDK 1.1. To download a copy of this release, go to http://www.sci-conservices.com/rel4/webpage/wwhome.html
xray is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures, Series and DataFrame: the xray DataArray and Dataset.
xray adopts the Common Data Model for self-describing scientific data in widespread use in the Earth sciences (e.g., netCDF and OPeNDAP): xray.Dataset is an in-memory representation of a netCDF file.
xray is being developed by Stephan Hoyer, Alex Kleeman, and other contributors.https://github.com/gmcgarragh/xdfv. Zebra (formerly named Zeb) is a system for data ingest, storage, integration and display, designed to operate in both real time and postprocessing modes. Zebra was developed by Jonathan Corbet and others in NCAR's Research Data Program.
Zebra's primary use is for the superpositioning of observational data sets (such as those collected by satellite, radar, mesonet and aircraft) and analysis products (such as model results, dual-Doppler synthesis or algorithm output). Data may be overlaid on a variety of display types, including constant altitude planes, vertical cross-sections, X-Y graphs, Skew-T plots and time-height profiles. The fields for display, color tables, contour intervals and various other display options are defined using an icon based user-interface. This highly flexible system allows scientific investigators to interactively superimpose and highlight diverse data sets; thus aiding data interpretation.
Data handling capabilities permit external analysis programs to be easily linked with display and data storage processes. The data store accepts incoming data, stores it on disk, and makes it available to processes which need it. An application library is available for data handling. The library functions allow data storage, retrieval and queries using a single applications interface, regardless of the data's source and organization. NetCDF data that conforms to Zebra conventions is supported by this interface.
Zebra is currently available to the university research community through the NCAR/ATD Research Data Program. Email requests to email@example.com. More information is on the web page http://www.atd.ucar.edu/rdp/zebra.html.
Unidata makes available a separate catalog to a directory of freely available, user-contributed software and documentation related to the netCDF library. This software may be retrieved by anonymous FTP. We haven't necessarily used or tested this software; we make it available "as is".
The criteria for inclusion in the netcdf/contrib/ directory of user-contributed software are:
The Space Time Pattern Mining toolbox contains statistical tools for analyzing data distributions and patterns in the context of both space and time. It includes a toolset for visualizing the data stored in the space-time netCDF cube in both 2D and 3D. Create Space Time Cube takes point datasets and builds a multidimensional cube data structure (netCDF) for analysis. Emerging Hot Spot Analysis then takes the cube as input and identifies statistically significant hot and cold spot trends over time. You might use the Emerging Hot Spot Analysis tool to analyze crime or disease outbreak data in order to locate new, intensifying, persistent, or sporadic hot spot patterns at different time-step intervals. The Local Outlier Analysis tool takes the cube as input to identify statistically significant clusters of high or low values as well as outliers that have values that are statistically different than their neighbors in space and time. The Utilities toolset enables you to visualize the data and analysis results stored in the space-time cube in two and three dimensions. These visualization tools can be used to understand the structure of the cube, how the cube aggregation process works, and to visualize the analytical results added to the cube by other Space Time Pattern Mining tools. See Visualizing the Space Time Cube for strategies to allow you to look at cube contents.
Applied Science Associates, Inc. has made the ASA View NC/Dap application freely available for download. ViewNcDap is a stand-alone research-based tool (with included demonstration data) that allows a user to visualize four dimensional NetCDF and OPeNDAP data. ViewNcDap is a Windows application that includes temporal/time step functionality for viewing animations of data that include temporal information. The application may be used to visualize a variety of time-varying geospatial scientific data in a simple map framework. It handles CF conventions and includes some aliasing features that could permit additional formats to be read. It should not be considered a GIS system, but is used to quickly preview a variety of data on a simple map. Data may also be filtered and saved to a local netCDF file.
Avizo software is a powerful tool for 3D data visualization and analysis. It offers a comprehensive feature set that addresses visualization, processing, analysis, communication and presentation. Avizo Green Edition includes an advanced set of features dedicated to climate, oceanography, environmental or earth-mapped data. It provides high-level support for the netCDF format, a dedicated Earth visualization module, and a set of advanced geographical projections applicable to a wide range of fast 2D and 3D data representations.
For more information, see www.avizo3d.com.AVS (Application Visualization System) is a visualization application software and development environment. An AVS module has been written that allows multi-dimensional netCDF data sets to read into AVS as uniform or rectilinear field files. The AVS user can point and click to specify the name of the variable in the selected netCDF file, as well as selecting the hyperslab. If 1D coordinate variables exist (a variable that has the same name as a dimension) then the coordinate variable will be used to specify the coordinates of resulting rectilinear field file. If no coordinate variable exists, then the resulting field file will be uniform. Once in AVS, there are hundreds of analysis and display modules available for image processing, isosurface rendering, arbitrary slicing, alpha blending, streamline and vorticity calculation, particle advection, etc. AVS runs on many different platforms (Stardent, DEC, Cray, Convex, E and S, SET, Sun, IBM, SGI, HP, FPS and WaveTracer), and it has a flexible data model capable of handling multidimensional data on non-Cartesian grids.
The module source code and documentation is available from the International AVS Center, in the ftp://testavs.ncsc.org/avs/AVS5/Module_Src/data_input/read_netcdf/ directory.
See also the information on DDI for another way to use netCDF data with AVS.
Barrodale Computing Services Ltd. (BCS) has developed a product that addresses one of the main objections heard from "technologists" (e.g., scientists, engineers, and other researchers) who avoid using databases to manage their data: "my very large data files are too cumbersome/difficult/slow/costly to load into a database". In addition to netCDF, these files come in a variety of formats (HDF5, GRIB, NITFS, FITS, etc.).
This BCS product is called the Universal File Interface (UFI); it's a database extension based on the IBM Informix Virtual Table Interface (VTI). (Please continue reading even if you don't have Informix running on your system, because IBM has just made available, at no charge, the Innovator-C Edition of Informix.) A demo that uses UFI to access wind speeds can be seen here.
VTI is a technology that supports making external datasets appear as tables to SQL queries and statements. UFI is a BCS database extension for delivering the contents of external data files as though they were rows in a database table. UFI makes a file look like a set of database tables, so "UFI managed tables" are actually virtual database tables. Consequently, users of UFI can perform SQL queries on their files without having to first load them into a database.
DioVISTA/Storm is a commercial software package that visualizes content of netCDF files as a time series of grids, isosurfaces, and arrows on a 3D virtual earth. Its user interface is similar to standard 3D earth visualizing software. It displays OGC KML files, Shapefiles, and online map resources through OGC Web Tile Map Services (WTMS). It supports CF Conventions version 1.6 (lon-lat-alt-time axis and trajectory). Its first version was released on Aug 5 2014.SuperComputer Systems Engineering and Services Company (SSESCO) has developed the Environmental WorkBench (EWB), an easy to use visualization and analysis application targeted at environmental data. The EWB currently has numerous users in the fields of meteorological research, air quality work, and groundwater remediation.
EWB system features include:
Systems currently supported include Win95, WinNT, OS/2, IBM RS/6000, Silicon Graphics, HP and SUN workstations.
SSESCO has implemented a meta-file layer on top of the netCDF library, called MeRAF. It handles multiple netCDF files as well as automatic max-min calculations, time-varying gridded, particle, and discrete data, logical groupings for discrete data, and an overall simplified and flexible interface for storing scientific data. MeRAF is being used by the DOE at the Hanford-Meteorological Site for observational data and will be used for their weather-modeling.
ESRI ArcGIS version 9.2 and later support accessing netCDF time-based and multidimensional data that follows CF or COARDS conventions for associating spatial locations with data. A selected slice of netCDF data may be displayed in ArcGIS as a raster layer, feature layer, or table. You can also drag a netCDF file from Windows Explorer and drop it in an ESRI application such as ArcMap.
FME, developed by Safe Software Inc., is a tool for transforming data for exchange between over 300 different formats and models, including netCDF. FME's read and write support for netCDF allows users to move data into the netCDF common standard, regardless of its source, and conversely enables end-users to consume netCDF data for use in their preferred systems. For more information visit http://www.safe.com/fme.
HDF Explorer is a data visualization program that reads the HDF, HDF5 and netCDF data file formats (including netCDF classic format data). HDF Explorer runs in the Microsoft Windows operating systems.
HDF Explorer offers a simple yet powerful interface for the visualization of HDF and netCDF data. The data is just a click of the mouse away. Data is first viewed in a tree-like interface, and then optionally loaded and visualized in a variety of ways. HDF Explorer features include fast access to data, grid, scalar and vector views. It also allows exporting your data either as an ASCII text file or a bitmap image.IDL (Interactive Data Language) is a scientific computing environment, developed and supported by Excelis Visual Information Solutions, that combines mathematics, advanced data visualization, scientific graphics, and a graphical user interface toolkit to analyze and visualize scientific data. Designed for use by scientists and scientific application developers, IDL's array-oriented, fourth-generation programming language allows you to prototype and develop complete applications. IDL now supports data in netCDF format.
As an example, here is how to read data from a netCDF variable named GP in a file named "data/aprin.nc" into an IDL variable named gp using the IDL language:
id = ncdf_open('data/april.nc') ncdf_varget,id, ncdf_varid( id, 'GP'), gpNow you can visualize the data in the gp variable in a large variety of ways and use it in other computations in IDL. You can FTP a demo version of IDL, including the netCDF interface, by following the instructions in pub/idl/README available via anonymous FTP from gateway.rsinc.com or boulder.colorado.edu. InterFormat is a medical image format conversion program with both Motif and character interfaces. InterFormat can automatically identify and convert most popular medical image formats and write output files in many standard medical image formats, or in formats such as netCDF that are suitable for input to leading scientific visualization packages. InterFormat runs on UNIX workstations; a version for OpenVMS is also available. A separate external module for IBM Data Explorer is available for use in IBM Data Explorer's Visual Program Editor.
For more details about the formats handled, program features, and pricing, see the Radio-Logic web site at <http://www.radio-logic.com>.
The Atmospheric and Oceanic Sciences Group at the National Center for Supercomputing Applications (NCSA) and the Mesoscale Dynamics and Precipitation Branch at NASA-Goddard Space Flight Center have developed the NCSA PATHFINDER module set for IRIS Explorer. Two of the modules, ReadDFG (to output Grids), and ReadDF (to output Lattices) are capable of reading from NCSA HDF files, MFHDF/3.3 files, and Unidata netCDF files. A user-friendly interface provides control and information about the contents of the files.
For ReadDF, the format translation is handled transparently. Up to five unique lattices may be generated from the file (as these files can contain multiple data fields) using a single module. A variety of dimensionalities and data types are supported also. Multiple variables may be combined in a single lattice to generate vector data. All three Explorer coordinate systems are supported.
With ReadDFG, user selected variables from the file are output in up to five PATHFINDER grids. Each grid can consist of scalar data from one variable or vector data from multiple variables. Coordinate information from the file is also included in the grids. Any number of dimensions in any of the Explorer coordinate types are supported.
For more information on the NCSA PATHFINDER project and other available modules, visit the WWW/Mosaic PATHFINDER Home Page at http://redrock.ncsa.uiuc.edu/PATHFINDER/pathrel2/top/top.html The ReadDF module may be downloaded either via the WWW server or anonymous ftp at redrock.ncsa.uiuc.edu in the /pub/PATHFINDER directory. For more information please send email to: firstname.lastname@example.org
See also the information on DDI for another way to use netCDF data with IRIS Explorer.
LeoNetCDF is a Windows application (Windows96/NT and higher) for editing netCDF files. It can display content of netCDF files in tree style control and permits editing its parameters in a standard Windows interface environment.
Mathematica is a technical computing environment that provides advanced numerical and symbolic computation and visualization. As of version 6, Mathematica adds classic netCDF data to the many forms of data it can import, export, and visualize.MATLAB is an integrated technical computing environment that combines numeric computation, advanced graphics and visualization, and a high-level programming language. Versions 7.7 and later of MATLAB have built-in support for reading and writing netCDF data. MATLAB version 2012a includes the netCDF 4.1.2 library with OPeNDAP client support turned on, so remote access to netCDF and other data formats supported by OPeNDAP servers is available.
For earlier versions, several freely-available software packages that implement a MATLAB/netCDF interface are available: nctoolbox, NetCDF Toolbox for MATLAB-5, MexEPS, the CSIRO MATLAB/netCDF interface, NetCDF reader, and fanmat.Noesys is software for desktop science data access and visualization. Available for both Windows and Power Macintosh platforms, Noesys allows users to access, process, organize and visualize large amounts of technical data.
Noesys can be used to:
Noesys has an interface to IDL®, allowing data to move back and forth between Noesys and IDL with the click of a mouse. Noesys includes the visual data analysis tools, Transform, T3D and Plot, for menu driven plotting, rendering, and image analysis. Noesys can import HDF, HDF-EOS, netCDF, ASCII, Binary, DTED, GeoTIFF, SDTS, TIFF, PICT, and BMP files, create annotations, macros, images, projections and color palettes specific to the data and save it the result as an HDF file. Noesys also includes an HDF-EOS Grid Editor. Noesys runs on Windows 95/98 & NT and Power Macintosh OS. More details and information about ordering Noesys are available from <http://www.rsinc.com/NOeSYS/index.cfm>.
Ryan Toomey reports:
Our website is http://www.originlab.com/
A general description of Origin: Origin includes a suite of features that cater to the needs of scientists and engineers alike. Multi-sheet workbooks, publication-quality graphics, and standardized analysis tools provide a tightly integrated workspace for you to import data, create and annotate graphs, explore and analyze data, and publish your work. To ensure that Origin meets your data analysis requirements, intuitive tools for advanced statistics, regression, nonlinear curve fitting, signal processing, image processing and peak analysis are built-in. Since any analysis operation can be set to automatically recalculate, you can reuse your projects as templates for future work, thereby simplifying your daily routine.
A general description of OriginPro: OriginPro offers all of the features of Origin plus extended analysis tools for statistics, 3D fitting, image processing and signal processing.
A general description of OriginLab Corporation: "OriginLab Corporation produces professional data analysis and graphing software for scientists and engineers. Our products are designed to be easy-to-use, yet have the power and versatility to provide for the most demanding user."Plot-Plus (PPLUS) is a general purpose scientific graphics package, which is used in several PMEL applications. It will read most standard ascii or binary files, as well as netCDF file format, which used by the TOGA-TAO Project and the EPIC system for management display and analysis. PPLUS is an interactive, command driven, scientific graphics package which includes features such as Mercator projection, Polar Stereographic projection, color or gray scale area-fill contour plotting, and support for many devices: X-windows, PostScript, HP, Tektronix, and others. This powerful and flexible package recognizes netCDF data format, and it can extract axis labels and graph titles from the data files. The user can customize a plots, or combine several plots into a composite. Plots are of publication quality. The PPLUS graphics package is used for all the TAO workstation displays, including the animations. The animations are created by generating a PPLUS plot for each frame, transforming the PPLUS metacode files into HDF format with the PPLUS m2hdf filter, and then displaying the resulting bit maps as an animation with the XDataSlice utility, which is freely available on Internet from the National Center for Supercomputing Applications, at email@example.com (184.108.40.206). There is also a new m2gif utility which produces GIF files from PPLUS metacode files.
PPLUS is supported for most Unix systems and for VAX/VMS, and is in use at many oceanographic institutes in the US (e.g., (PMEL, Harvard, WHOI, Scripps, NCAR, NASA, University of Rhode Island, University of Oregon, Texas A&M...) and also internationally (Japan, Germany, Australia, Korea...).
Plot Plus is now available at no charge. It does require licensing on a per computer basis, but the license is at no cost. For more information about licensing, see http://dwd6.home.mindspring.com/pplus_license.html/; source and documentation are available via anonymous FTP from ftp://ftp.halcyon.com/pub/users/dwd/pplus1_3_2.tar.gz and ftp://ftp.pmel.noaa.gov/epic/manual-dir/pplus.pdf.
Email: firstname.lastname@example.org Postal mail: c/o Donald Denbo 2138 N 186th St Shoreline, WA 98133 Fax and Voice: (206) 366-0624PV-Wave is a software environment from Visual Numerics for solving problems requiring the application of graphics, mathematics, numerics and statistics to data and equations.
PV-WAVE uses a fourth generation language (4GL) that analyzes and displays data as you enter commands. PV-WAVE includes integrated graphics, numerics, data I/O, and data management. The latest version of PV-Wave supports data access in numerous formats, including netCDF.
See also the information on DDI for another way to use netCDF data with PV-Wave.Slicer Dicer is a volumetric data visualization tool, currently available for Windows and under development for other platforms. The Slicer Dicer Web site includes a complete list of features, an on-line user's guide, and examples of Slicer Dicer output. Visualizations features include:
Surfer is a full-function contouring, gridding and 3D surface mapping visualization software package. Surfer's sophisticated interpolation engine transforms XYZ data into publication-quality maps. Surfer imports from and exports to a multitude of file formats, including NetCDF grids.
vGeo (Virtual Global Explorer and Observatory) is an end-user product from VRCO designed to import and visualize multiple disparate data sets, including computer simulations, observed measurements, images, model objects, and more. vGeo is available for IRIX, Linux and Windows platforms and supports displays ranging from desktop monitors to multi-walled projection systems. It accepts data in a variety of formats, including netCDF, and allows the user to specify how multiple files and variables are mapped into a data source. 3D graphics are built from the underlying data in real-time, and the user has interactive control of graphics, navigation, animation, and more.
VISAGE (VISualization, Animation, and Graphics Environment) is a turnkey 3D visualization system developed at General Electric Corporate Research and Development, (Schroeder, WJ et al, "VISAGE: An Object-Oriented Scientific Visualization System", Proceedings of Visualization `92 Conference). VISAGE is designed to interface with a wide variety of data, and uses netCDF as the preferred format.
VISAGE is used at GE Corporate R & D, GE Aircraft Engine, GE Canada, GE Power Generation, as well as ETH Zurich, Switzerland, MQS In Chieti, Italy, and Rensselaer Polytechnic Institute in Troy, New York.
GE has another application called "Decimate" that does polygon reduction/decimation (Schroeder,WJ et al, "Decimation of Triangle Meshes", Proceedings of SIGGRAPH `92). This application uses netCDF as a preferred format. Decimate is currently licensed to Cyberware, Inc., makers of 3D laser digitizing hardware. Decimate is currently bundled with the scanners, and will soon be available as a commercial product.
Makai Voyager, developed by Makai Ocean Engineering, Inc., is 3D/4D geospatial visualization software that enables users to import, fuse, view, and analyze large earth, ocean, and atmosphere scientific data as it is collected or simulated in a global geo-referenced GIS platform. The key differentiator of Makai Voyager is its level-of-detail (LOD) technology that enables users to stream big data rapidly over a network or the web.
Features in Makai Voyager Version 1.2 include:
Individual or group licenses are available for Windows (32- and 64-bit), Linux, and Mac OS X. A full-featured 30-day trial version of Makai Voyager is available for download.