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Pretty common occurrence with that type of motion for occlusion using 1 Kinect, dual Kinects give much better tracking results, but you need 2 computers that will handle the Kinect v2, calibration comes into play, and you will loose capture volume, or need a larger area to record in, more info on this in the iPi Docs also.
In my opinion, Dual Kinects are the way to go for any capturing, if wanting to use Kinects, if you have the minimum area and meet the requirements needed to use Dual or more.
You will most likely never get a perfect tracking without some bad areas that need to be fixed, but the good thing is, iPi Studio allows this to be done fairly easily once you get the hang of it.
Most tracking issues can be cleaned up right in iPi if you stop the tracking right when it looses track, switch to the IK Tool, and reposition the arm/leg and hit the refit button, then continue until tracking is lost again.
If it keeps loosing track, and the tracking process has passed these occlusion areas, you can go to the areas affected and using frame advance with the > key and pull each arm/leg key closer to the arm/leg cloud through the area, (you will of course either need to guess a close trajectory here, or use the video reference to help), then once past the bad areas, let the program take over again hitting track forward again. This can be done with any arm or leg issue such as this. (NOTE: DO NOT rerun the track forward process on the areas you just manually fixed, it will just mess up and undo what you just manually set).
You can spin the camera to view better for alignment during this step, then hit Camera 1 button again to start tracking from forward view.
In fully occluded areas, using the IK tool to reposition the arm(s)/leg(s) as above, but don't let the tracking run again on those areas, just go on by them after manual repositioning, using the Refine button in later steps should help maintain where you manually positioned those areas, but possibly not in the areas where the cloud data is totally invisible, then only manual re-setting will apply, no auto correct features will work.
For now you don't seem to have any Move controllers, or the dongles (unless maybe you are using a laptop with built-in Bluetooth may work now) but Move controllers are recommended for better final tracking results, but have no effect on the initial tracking quality, the data is added as a second step after tracking is completed, or at least the full area of the ROI take you want is completed.
If you do use Moves, you will most likely need 1 on the head also for better head tracking with Kinect sensors using some kind of device to hold it in place, but you can use manual head positioning later on with certain "frame advancing tricks" in iPi, or another editor also, I am sure there are some YouTube tutorials to assist with this.
Once you have the initial corrections made throughout the ROI, you can then run the Refine feature (Forward or Backward or Both ways) if you do use Moves, you should learn how to Add and position them correctly in scene first (see iPi Docs) and apply their Data before running the Refine feature, as the hand rotations should remain and you will get better Refined results.
Once you get the majority of the capture looking pretty good throughout, you can then fix any further small areas by sliding the ROI to only encompass the smaller bad areas and try to rerun the above steps just on those areas, or if not too bad, you can just move on.
Then run the Jitter Removal and set its parameters first to what you want, if you do use Moves, make applying their Data the final step and should be rerun if any additional manual corrections have been made to the main skeleton after applying their Data before you export the motion.
Use an external 3D editor to complete any offsets needed, and of course depending on the character used with the mocap, you will need to do this anyway.
Hope this helps and maybe some other experienced Kinect users will add their thoughts to further help.
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