tweak plot-ave-arrow to have white background, custom color map and better figsize
Tested everything on bennet.
Merge /home/jeffschulte/sim-protein
Merge /home/jeffschulte/sim-protein
remove generated pdf files from repository
Tested everything on bennet.
Merge /home/jeffschulte/sim-protein

Conflicts:
	Makefile
	data/shape-randst/plots/box-plot_D--randst-25-800-800-9500-1500-exact.pdf
	paper/plot-ave.pdf

Tested everything on bennet.
Merge /home/jeffschulte/hierarchical-protein
changed file structure got rid of a lot of files
Tested everything on quipu.
deleted a lot of files and edited protein microscopy to make file structure correctly for time-map
Tested everything on quipu.
Merge /home/jeffschulte/hierarchical-protein

Conflicts:
	paper/plot-ave.pdf

Tested everything on bennet.
changed a lot of python files to work with new file structure
Tested everything on quipu.
changed a lot of python files to work with new file structure
Tested everything on quipu.
Merge branch 'master' of ../../droundy/git/protein
made changes necc for Makefile to work with new file structure
Tested everything on quipu.
added data for smeared single image plot
Tested everything on quipu.
added deterministic data to plot-arrow-ave
Tested everything on wentworth.
fixed ave-plot to have good size
Tested everything on wentworth.
added some plots to the paper and altered pretty much every plot in the paper
Tested everything on quipu.
added captions to paper, added scale bar to plot-arrow-ave
Tested everything on quipu.
wrote text in Mannik and stadium shape section
Tested everything on quipu.
edited text in Mannik section and adjusted size of paper/plot-arrow
Tested everything on quipu.