Determining deflection of a cylinder

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I have a cylinder of length l and radius r and I am trying to work out how far off straight it is. (What I mean by that is assuming the other end of the cylinder is at 0,0 what is the deflection from end to end. Does that make sense? I'm sorry I'm having trouble finding a good word to explain it. I hope it is clear otherwise ask in the comments.)

I can get the x, y (and maybe z, if it's possible to solve without the z then please explain how to do it that way) of 5 points from the circumference of the cylinder. How would I work out how straight it is from this information?

I'm thinking that it may be solvable by determining the ellipse created by the angle and then working out the angle by knowing that it should be a circle. Is that right? how would I do this?

Thanks a lot!


Some clarification on what I mean:

This is the setup, Imagine the x axis going into and out of the screen, the y axis going up and down and the z axis going left and right. Now assuming it was directly along the z axis (ie straight) when we looked along the z axis we would see a circle like so. However if it was not directly along the z axis, say the end was slightly (a lot in the example picture) higher in the y axis we would see this. This is still viewing it directly along the z axis, it's just the cylinder no longer goes directly along the z axis. The shape at the end is no longer a circle when viewed like this, as you can see. If we had x,y coordinates of several points (I can get as many as needed, fewer is best, but accuracy is key) on that ellipse's circumference, could we determine the elevation along the x and y axis as compared to straight along the z axis? How would we determine it if we had the x, y and z coordinates?