Overview:

This library provides a high-level Clojure interface to the HDF5 library for storing scientific data. It is built on top of the JHDF5 library, which provides a high-level Java interface. While JHDF5 can be used directly from Clojure, this additional layer adds a lot of convenience:

• Uses Clojure vectors rather than Java arrays for array I/O.
• Multimethods reduce the huge Java API to just a few functions.

This library is work in progress. Only scalar and 1D array data are supported at the moment, both for datasets and attributes.

Building:

This build depends on a local jar for JHDF5. Build is managed by Leiningen, and the local jar dependency is resolved by creating a local maven repository more or less like:

mvn deploy:deploy-file -DgroupId=cisd -DartifactId=jhdf5 \
-Dversion=13.06.2 -Dpackaging=jar \
-Dfile=/path/to/cisd-jhdf5-batteries_included_lin_win_mac_sol.jar \
-Durl=file:repo

Building Documentation:

API documentation can be rebuilt using leiningen and codox:

lein doc

Basic Usage:

;; Create and open a new HDF5 file / storage container
(def myh5root
     (create (clojure.java.io/file "/path/to/file.h5")))

;; Open an existing HDF5 file (read-only)
(def myh5root
     (open (clojure.java.io/file "/path/to/file.h5")))

;; Open an existing HDF5 file (read-write)
(def myh5root
     (open (clojure.java.io/file "/path/to/file.h5" :read-write)))

;; Close a file
(close myh5root)

;; Create a group in an HDF5 file
(create-group myh5root "examplegroup")

;; Create an attribute of the HDF5 root /
(create-attribute myh5root "myattribute" "some value")

;; ... more

Links:

HDF5

http://www.hdfgroup.org/

JHDF5

https://wiki-bsse.ethz.ch/display/JHDF5/JHDF5+(HDF5+for+Java)