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.

Notes on JHDF5:

This library uses CISD's JHDF5 libraries. We have published these libraries to clojars.org for your convenience. Solaris is at the moment not supported.

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)