Both the ArduPilot system and the MatrixPilot system perform wind estimation internally. Here is a link to the MatrixPilot system, software includes Peter's flight analysis program and instructions for using it. I do not have a separate Excel analyzer. The MatrixPilot software performs the wind estimation computations in flight and logs all flight data. Peter's "python" script converts the raw data into Excel format and Google Earth format.
By the way, for a balloon, I would think estimating the wind would be rather easy, you simply take the speed over ground output of a GPS, it will pretty much be equal to the wind, and course over ground will be the direction the wind is blowing in.
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