usage: prog [options] <untilted micrograph> <tilted micrograph>....
This is a tilted - untilted particle particle picker, for use in RCT particle picking. A tilted and untilted micrograph are loaded and the user picks a untilted particle and a corresponding tilted particle.
After atleast 3 particle pairs are picked a transformation matrix is completed which can be used to predict the postion of the tilted or untilted particle from a untilted or tilted particle respectily.
From the transform matrix, the tilt angle, tilit axis(with respect to Y) and the gamma angle are all computed. 
The program uses the mediator pattern. The mediator, a RCTboxer object HAS A strategy(itself a strategy pattern), HAS A set of windows(in this case 2, but more can be added), HAS A control pannel, and
HAS a particle list. The strategy object implements the strategy pattern(currently a maunal and a pair picker strategy are implemented). This code is in 'emrctstrategy'. The control pannel object HAS A strategy
widget(so there must be one widget for each strategy) and the strategy GUI widget and the strategy itself are tightly coupled. The window object each HAS A EMBoxList, which is a composite of EMBox objects.
(A class diagram is located in my lab notebook, page16)
Usage: e2RCTboxer.py untilted.hdf tilted.hdf options.

Option Type Description
--version None show program's version number and exit
--boxsize, -B int Box size in pixels
--write_boxes None Write coordinate file (eman1 dbbox) files
--write_ptcls None Write particles to disk
--format None Format of the output particles images, should be hdf
--shrink int Shrink the images by an integer, uses math.meanshrink
--norm str Normalization processor to apply to written particle images. Should be normalize, normalize.edgemean,etc.Specifc "None" to turn this off
--invert None If writing outputt inverts pixel intensities
--suffix str suffix which is appended to the names of output particle and coordinate files
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness

For more information go to emanwiki/EMAN2/Programs/e2RCTboxer.