Improved Documentation

also improved peak finding for double gaussian
show negative OD and edits to fring_fit

Instead of showing absolute values in OD image, now the actual values
are used because we have negative numbers in the OD images .
added code to produce nice average image for ben
removed windows-only code
Commented out useless code in cloud_distribution and fixed some guess related bugs
calculate sample position statistic
Latest version 12/2/2014
made loading .mat files compatible to mac os

Made a switch for switching to Mac OS. The only difference is the
format of the directory for .may files.
Added new switch OVERLAP

change OVERLAP to True will fit the data to one gaussian but assume
that they are two gaussians of equal height and width overlapping. The
output will have two extra lists ‘h_from_sample’ (height of atoms from
sample) and ‘d_peaks’ (inferred distance between two gaussians that are
overlapping).
Merge branch 'mac_testing' into testing
cloud_width

Moved the variable cloud_width to the top of the code. This variable is
the assumed sigma of the atom clouds in z-direction. We need to use it
for OVERLAP mode.
automated checking for MAC OS

platform.system() returns ‘Darwin’ if Mac OS.\
Merge branch 'testing'

Conflicts:
	cloud_distribution.py