Finding angle of swinging Double pendulum

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Hi there,
I am struggling to calculate the angle between the hinge joint of a double pendulum (the flexion angle). I recorded the data on a motion capture system using markers. (Please see pic below to show vectors and markers). I created vectors in order to calculate the angle in the same plane to the pendulum swing. The reference vector is taken when the pendulum is held static in a straight vertical line. The ''dyn'' vectors refers to when the pendulum is swining chaotically. I have seperated the double pendulum into two single pendulums (top portion is one single pendulum and bottom portion is another single pendulum).
How would I go about calculating the joint angle? I am trying to simulate a knee joint with a double pendulum, so am trying to get the angle around the hinge joint (the flexion angle).
I have attached the code I have so far. I thought that the angle between the joint would be Bottom_Alpha-Top_Alpha, however this does not seem to be correct? The angle I am interested in, is the alpha angle in the matlab files.
I have included the workspace so you only need to run the calculate_angles file, but the other files are there for reference.
Please let me know if you need any clarification.
Thanks so much in advance for any help, really appreciate it.

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