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This phase spins the scene around the vertical axis to align two trackers to the heading you desire. To use it, select two trackers and click the Store Trackers button. If you think of a line from one tracker to the next, this phase positions that line, as seen from above, to point in the direction you want.
If you specify an angle of 0, the line will point along the positive X axis. At 90 degrees, it will point along the positive Y axis, etc. To achieve this, the phase rotates the whole scene about the vertical axis, keeping the midpoint between the two trackers stationary.
This phase can be used once you have set up a ground plane, to orient the scene so that some trackers are parallel to one of the axes (or at any other angle). Because the phase rotates about the Z axis, it will not interfere with your existing ground plane setup.
The phase shows which direction the line between trackers is headed: Tracker1>Tracker2 means it goes from Tracker1 to Tracker2. If you'd rather it goes the other way, click the Reverse checkbox. That will wind up rotating the scene 180 degrees.
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