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FIBER WALK DEMO

The Fiber Walk class to run a Fiber Walk simulation.

The demo uses:
- the networkX package (http://networkx.lanl.gov/)
- the numpy package (http://sourceforge.net/projects/numpy/)
- the scipy package (http://www.scipy.org/SciPy)
- the classes Lattice and FiberWalk written by Alexander Bucksch

Note: The graphics shown in the paper where generated with mayavi2
(http://docs.enthought.com/mayavi/mayavi/index.html)

The code is free for non-commercial use.
Please contact the author for commercial use.

Please cite the Fiber Walk Paper if you use the code for your scientific project.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0085585
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Author: Alexander Bucksch
Department of Plant Biology
Warnell School of Forestry and Natural Resources
Institute of Bioinformatics
University of GEorgia, Athens

Mail: bucksch@uga.edu
Web: http://www.computational-plant-science.org
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Copyright (c) 2012, 2016 Alexander Bucksch
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

  * Redistributions of source code must retain the above copyright
    notice, this list of conditions and the following disclaimer.

  * Redistributions in binary form must reproduce the above
    copyright notice, this list of conditions and the following
    disclaimer in the documentation and/or other materials provided
    with the distribution.

  * Neither the name of the Fiber Walk Demo Developers nor the names of its
    contributors may be used to endorse or promote products derived
    from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

'''


INSTRUCTIONS

Running the demo:

1.) make sure you have python 2.3, numpy 1.3, scipy 0.9 and networkX 1.7 properly installed
The Demo may run with older versions, but no guarantee 

2.) copy the files Lattice.py, FiberWalk.py and main.py to a folder your choice.

3.) on the command line, go to the folder of your choice

4.) type: python main.py

5.) The program generates saves plots in the creates subfolder FiberWalks and python pickles of the walk data in the folder you have chosen.

6.) Happy Walking!

Changing walk parameters:

1.) open main.py in a text editor

2.) search for the following section

#Fiber Walk parameters    
dimension = 2 # choose dimension
numberOfSteps = 100 # choose the length of the walk
numberOfObjects = 5 # choose number of walks to be generated
numberOfContractions = 1 # choose number of contractions per step

3.) adjust the variables as you wish

4.) save the file and run the demo

5.) Happy Walking!