NavigationData timestamps should originate at a lower level than mitk::TrackingDeviceSource::GenerateData() since this method could be called well after the time the tracking device made the position/orientation measurement. I think the mitk::TrackingDevice should be responsible for setting a timestamp on the mitk::TrackingTool. With this approach the mitk::TrackingDeviceSource::GenerateData() method would just need to transfer the timestamp from the mitk::TrackingTool to the mitk::NavigationData ouput.
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Feature was implemented in bug-16065-TimestampsTrackingtools, it will be integrated into the master soon