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Many fixes for the frame_order.permute_axes user function.

The z-axis inversion is now encoded into a 3D numpy array as the index of the new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be reintroduced later).

bugman 2014-09-10

changed /branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Diff Switch to side-by-side view
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