Changed the names of the files so that they will work.  Modified location of input files.  Added instructions to the README.
Merge branch 'master' of ssh://login.cs.unc.edu/afs/unc/proj/stm/src/git/SpindleSimScript
Updating README.
Changed from using spheres for the kMT plus ends to point sets

One point set is used for each end of the spindle. This is much
faster to load and produces more accurate fluorescence images
because the fluorophores are located at the exact positions in
the simulation file whereas the single fluorophore on the sphere
was located anywhere on the surface of the 20nm diameter sphere
used to represent the point.

Added a function to produce the XML for one end of the spindle
to reduce code redundancy.
Added a Windows batch file to generate a fluorescence animation
Merge branch 'master' of github.com:cquammen/SpindleSimScript

Conflicts:
	README
Re-enabled generation of the microtubule cylinders.
Removed errant git hash
Added spindle diameter and ktm sphere of uncertainty feature requested by Andrew Stephens
Set disk fluorophores to fixed number instead of fixed density
Added test CSV file with all zeros
Fixed random kmt spherical offset

Also removed an unused parameter from initialize_cylinder function.
Added randomPointInSphere function
Added two more kinetochore florophores at each kinetochore location

They have independent radii and uncertainty sphere radii
Improved names of checkboxes and menus

Also gave the main window a better title.
Cleaned up how parameters are passed around

Parameters from the GUI are stuffed in a single data structure that
gets passed around.
Adding the second and third sets of fluorophores is optional
Organized the GUI widgets a bit better
Merge pull request #1 from cquammen/master

Some changes to merge