Overview

Woolz is the name (not an acronym) for a set of image processing software. The Core software is organised as a series of libraries for application development and a set of Command-Line Binaries which can be used for simple image processing or embedded in scripts for more complex operations. Large scale applications with graphical user-interfaces such as Reconstruct or MAPaint are documented elsewhere. The source code is maintained under git and is available as open-source (under the general GNU GPL 2 licence) Either from the EMAP site or from github. Bug and issue reporting should be done through thea github issues page. This documentation is generated using Doxygen and is available from both EMAP and github.

The best way to use this documentation is to open the "Modules" menu-folder in the index on the LHS browser window. If you simply want to use the command-line binaries then select "Basic woolz operations", "Data Format Conversion" or "Extended Applications". These each expand to a list of the binaries available for which there is a manpage-style page available. In each case there will be (not yet complete) example usage and a brief description. If you are interested in using the library functions then consult the library modules and browse for the required function. Example usage is most easily found in the set of binaries available with the source code.

This documentation provide manuals and code documentation for the core libraries and associated command-line binaries. Using these binaries sophisticated image-processing applications can be developed and prototyped using standard unix scripting. In addition the libraries have a Java binding to allow the use of very fast and efficient C-code with a Java interface.

More detail of the code can be found in the sub-sections Command-Line Programmes and Software Libraries. Compiled versions and source code can be obtained from the EMAP web-site www.emouseatlas.org.

Structure

The woolz software is organised as a series of software libraries with a hierarchical dependency. The compiled binaries are compiled against these libraries with in some cases link to other non-system libraries such as libtiff and libjpeg. The source code is organised as a series of directories, one for each library and programme group. The set of directories is:

binWlz - simple command-line binaries which typically execute a single woolz library function
binWlzExtFF - commmand-line binaries for data format conversion
binWlzApp - more complex programmes for image programming
libAlc - library for memory allocation and memory management
libAlg - library of numerical algorithms
libWlz - basic image processing operations, the core of the woolz image processing system.
libWlzExtFF - library for format conversion and I/O to different image standards.
libbibfile - "bibtex" formmat file handling, used for many standard metadata files generated by woolz applications such as MAPaint and Reconstruct
libhguDlpList - library implmenting functions to create and manipulate doubly-linked lists.
libReconstruct - obselete library for image registration and alignment, \ now incorporated into linWlz.
libWlzBnd - library for special Java bindings as part of the Java Woolz automated mapping.