1. A system to analyze a geometry of a radiation treatment apparatus to determine a location of an origin and an orientation of a coordinate system used to reference radiation beam and patient positioning so that a treatment plan can be more accurately applied to the patient, the system comprising: a radiation treatment apparatus including a plurality of rotating assemblies each to direct a radiation beam through a target of a patient and each having a rotational path in a distinct plane and an axis of rotation, the axis of rotation of each rotating assembly intersecting the axis of rotation of each other rotating assembly of the plurality of rotating assemblies at a substantially same three-dimensional coordinate defining an isocenter of an isocenter coordinate system of the treatment apparatus; a plurality of optically trackable bodies, each connected to a preselected portion of a respective one of the plurality of rotating assemblies of the treatment apparatus, and each having a plurality of optical retro-reflective spheres mounted thereto; an optical detector having an optical detector body positioned spaced apart from the plurality of optically trackable bodies at a selected three-dimensional optical detector reference location and at least a pair of separate and spaced apart optical receivers connected to the optical detector body, each of the at least a pair of optical receivers positioned to receive optical energy reflected by a subset of the plurality of optical retro-reflective spheres of the optically trackable bodies to detect a three-dimensional sphere position of the plurality of retro-reflective spheres so that during rotation of the plurality of rotating assemblies the optical detector produces a plurality of position signals indicating three-dimensional coordinate positions for the plurality of optical retro-reflective spheres, and a determiner in communication with the optical detector to determine the isocenter of the radiation treatment apparatus, the determiner having memory associated therewith and geometry analyzing software stored in the memory to analyze radiation treatment apparatus geometry, the geometry analyzing software including: a position determiner responsive to the plurality of position signals from the optical detector to determine a respective set of three-dimensional coordinate positions for each one of the plurality of rotating assemblies, each set of three-dimensional coordinate positions located substantially along the rotational path of the preselected portion of each respective one of the plurality of rotating assemblies, an arc determiner responsive to the position determiner to determine a fit of a separate arc to each set of three-dimensional coordinate positions for each respective one of the plurality of rotating assemblies, each fitted arc indicating the rotational path of the preselected portion of a respective one of the plurality of rotating assemblies and positioned in a plane substantially orthogonal to that of each other fitted arc, an axis determiner responsive to the arc determiner to determine a center of rotation and a normal for each fitted arc indicating the axis of rotation of each respective one of the plurality of rotating assemblies, and an intersection determiner responsive to the axis determiner to determine an intersection of the axis of rotation of each of the plurality of rotating assemblies, the intersection substantially indicating the three-dimensional coordinate position of the isocenter.