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Fundamentally a joint trajectory is a matrix of points and a matching vector of time offsets (in sections from the start of the trajectory) which give each row of the matrix a point in time. You could write these out to a CSV file fairly easily from a ROS node.

However taking a step back I don't think filtering out these glitches is the best idea, they are probably caused by a bug in your code or error in your maths. There is no reason why you shouldn't be able to produce a perfectly smooth (and tangentially continuous) joint trajectory path. So I would concentrate your efforts there, and hopefully you will not need an additional filtering step.