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Atmospheric Toolbox is a set of Matlab tools for accessing, analyzing, and visualizing atmospheric data. Large datasets, complex data formats, and incompatible tools can make atmospheric analysis complicated. The Atmospheric Toolbox addresses these challenges.
- Matlab 2012a or newer (with Image Processing Toolbox)
- Java 6
Download the latest version here or from the command line:
git clone https://github.com/atmospheric/atmospheric.git
Download the sample data (optional), which is helpful for running the tutorials and unit tests:
git clone https://github.com/atmospheric/sampledata.git
In Matlab, change to the directory containing the toolbox and run the setup:
cd ~/workspace/atmospheric
setupAtmospheric()
The Windows version of Matlab and the Netcdf v4.3 libraries use conflicting versions of protobuf.jar. This is resolved by configuring Matlab's Java static classpath to load the newest version of protobuf.jar.
Create or open your preferences file:
edit(fullfile(prefdir,'javaclasspath.txt')) % Matlab 2012b and newer
edit(fullfile(prefdir,'classpath.txt')) % Matlab 2012a and older
Append these lines to your preferences file:
<before>
c:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\protobuf-java-2.4.1.jar
Restart Matlab, call javaclasspath('static'), and verify protobuf-java-2.4.1.jar is the top entry.
Lastly, change to the directory containing the toolbox and run the setup:
cd ~/workspace/atmospheric
setupAtmospheric()
For more permanent installation, call the setupAtmospheric() from your startup.m file.
If everything went well, you should see the following text displayed at startup:
NCTOOLBOX added to Matlab path
ATMOSPHERIC added to Matlab path
The toolbox is ready-to-use for Matlab 2012a and newer; older versions of Matlab can be supported, but require some additional manual configuration. For Matlab versions 2011b and older, create a copy of your classpath.txt (this is the same as javaclasspath.txt for newer versions of Matlab), place it in your startup directory, and edit to include the following lines:
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\udunits-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\udunits-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\slf4j-log4j12-1.7.2.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\slf4j-api-1.7.2.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\quartz-2.1.6.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\protobuf-java-2.4.1.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\opendap-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\netcdf-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\log4j-1.2.17.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\joda-time-2.1.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\jna-3.0.9.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\je-4.0.92.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\jcl-over-slf4j-1.7.2.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\jcip-annotations-1.0.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\grib-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\ehcache-core-2.6.5.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java\bufr-4.3.15.jar
C:\pathToYourWorkspace\atmospheric\matlab\external\nctoolbox-20130305\java
Restart Matlab, and call javaclasspath to verify the entries are present in your STATIC JAVA PATH (not the dynamic path).
To run the unit tests, check out the source code along with the sampledata repo, then from Matlab call:
TestAtmospheric.all();