Are positive and negative angles defined for three dimensions

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In two dimensions, the anticlockwise direction is considered to be positive and the clockwise direction is considered to be negative. Does this hold even for angles in 3 dimensions?

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In 3 dimensions, you'll have to specify the axis of rotation. This means that you have 3 vectors involved: The two vectors $a$, $b$ for which you want to determine the angle, and the axis $r$ around which you are rotating.

Whether the rotation is clockwise or anti-clockwise is a matter of definition. For example, if you look at a clockwise rotation from above, then it will be anti-clockwise when you look at it from below. This is the reason for why you need a 3rd vector (or some other means) to determine clockwise-ness.

One way to determine whether a rotation is clockwise, could be to define clockwise-ness depending on whether

$$\operatorname{sign}(\det(a, b, r)) \tag1$$

is $1$, $-1$ or $0$. where $0$ basically means "undefined". The latter case occurs when one vector is 0, or when $a=\lambda b$, that is if the angle is $0^\circ$ or $180^\circ$. It also occurs if $r$ is in the plane spanned by $a$ and $b$.

Notice that $\det$ is alternating multi-linear, thus the sign of $(1)$ will flip when $a$, $b$, $r$ are permutated by an odd permitation. It also flips when one of the involved dectors is replaced by its negative, for example flipping $r$ will flip clockwise-ness: $$\operatorname{sign}(\det(a, b, -r)) = -\operatorname{sign}(\det(a, b, r)) $$ etc.

Also notice that one $r$ won't work for all $a$ and $b$. For example, if $a$, $b$ and $r$ are linerly dependent, then you'll get the "undefined" case. This means you are looking at the rotation edge-on.