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Is it possible to track multiple LED's?
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Are you referring to tracking markers with PPT? If so, it is possible to have multiple markers tracked in PPT and streamed to Vizard via VRPN. The following page has example code for connecting to multiple markers by number:
http://docs.worldviz.com/vizard/#WorldViz_PPT_VRPN.htm
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when I rotate the map 90 degrees in Yaw of the map, it appears to be 90 degrees pitch
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Please describe your hardware setup in more detail. Do you have an orientation sensor? How is it mounted to the HMD? In Vizard, you may need to add an orientation offset and reset the sensor so it is aligned with the coordinate system of the position tracker.