alternaria -- fit cylinders and ellipsoids to fungus
 ====================================================

 Fits connected ellipsoids and cylinders to the structure of fungus imaged under
 a microscope in a 3-D stack. The structure follows a grammar for growth
 specific to Alternaria, a genus of fungus. The images are explained with a
 probabilistic generative model over the structure of Alternaria and the camera
 capturing it. Samples of geometric parts, their topology, and microscope
 parameters are generated during statistical inference, simultaneously fitting
 instances of the structure and camera to an image stack. Additional tools are
 included to generate and view structure models.

 Build the program by running 'configure' followed by 'make'. See the INSTALL
 file for information on how to use a configure script. If there is no configure
 script, see further below how to generate one. 

 Depends on libjwsc, libjwsc++, OpenGL, and GLUT. Needs GLUT for the viewer and
 gnuplot for plotting.

 Documentation can be generated from the source code with Doxygen. 

 Refer to 'alternaria -h' for usage. 

 Comments welcome --> Joseph Schlecht <schlecht@uni-heidelberg.de>


 Building from SVN
 =================

 To build the sources from svn checkout, you need to do two things: (1) checkout
 the m4 macros and (2) build the configure script with autotools.

 1. Checking out the m4 macros

    The autotools used to build the configure script need a set of macros
    written in the m4 language and expect them to be installed in a directory
    'libjwsm4' at the same level as this program. The macros are shared by other
    programs and, if you haven't already done so, you will need to check them
    out.

    Change to the directory containing this program and execute
    
        svn co ${SVN_ACCESS}${SVN_REPOSITORY}/src/libjwsm4/trunk libjwsm4

    where SVN_ACCESS is probably either 'svn+ssh://host' or 'file:///' and
    SVN_REPOSITORY is the path to the svn repository.

    Then a directory listing would look like this

        alternaria
        libjwsm4
        ...

 2. Build the configure script using autotools

    The configure script is an sh shell script that can run on just about any
    machine. It checks for the availability of other packages that the
    library depends on. Those checks are primarily constructed using the m4
    macro language, which is expanded into sh.

    To build the configure script, you need the autotools programs. If
    installed, the following set of commands will generate the configure
    script

        aclocal -I ../libjwsm4 ; autoheader ; automake -a ; autoconf

    Use the generated configure script to build the library.