So that we're clear on definitions: A pair of diameters of an ellipse are conjugate if (and only if) the tangents at the endpoints of one diameter are parallel to the other diameter.
Let $P(a \cos\theta, b \sin\theta)$ be a point on an ellipse in standard position (for now). The tangent line at $P$ has slope vector $(-a\sin\theta, b\cos\theta)$; because this can be written $(a\cos(\theta+\pi/2), b\sin(\theta+\pi/2))$, we see that it is also the position vector of a point, say $Q$, on the ellipse. The diameter through $P$ is conjugate to the diameter through $Q$.
Therefore, if we have $P(p_x, p_y)$ and $Q(q_x, q_y)$ as endpoints of conjugate diameters of an ellipse in standard position (with $\angle POQ < \pi$ a counterclockwise angle), we can write:
$$\begin{align}
p_x = \phantom{-}a \cos\theta &\qquad p_y = b \sin\theta \\
q_x = -a\sin\theta &\qquad q_y = b\cos\theta
\end{align}$$
for some $\theta$, so that
$$a^2 = p_x^2 + q_x^2 \qquad\qquad b^2 = p_y^2 + q_y^2 \qquad\qquad (\text{and}\quad p_x q_y - p_y q_x = a b)$$
If the ellipse in question is rotated, things are a little more complicated.
We take $P$ and $Q$ to be the images of $(a\cos\theta, b\sin\theta)$ and $(-a\sin\theta, b\cos\theta)$ under rotation by angle, say, $\phi$. Using an appropriate rotation matrix, we have
$$\begin{align}
p_x = \phantom{-}a \cos\theta \cos\phi - b \sin\theta \sin\phi &\qquad
p_y = \phantom{-}a \cos\theta \sin\phi + b \sin\theta \cos\phi \\
q_x = -a \sin\theta \cos\phi - b \cos\theta \sin\phi &\qquad
q_y = -a \sin\theta \sin\phi + b \cos\theta \cos\phi
\end{align}$$
These provide relations
$$\begin{align}
p_x^2 + p_y^2 + q_x^2 + q_y^2 &= a^2 + b^2 &=: r \\
p_x q_y - p_y q_x &= a b &=: s
\end{align}$$
(The latter actually re-captures a result, cited by Isaac Newton, that all "bounding parallelograms" of an ellipse have the same area.)
Thus,
$$\begin{align}
a + b &= \sqrt{a^2 + b^2 + 2 a b} = \sqrt{r + 2 s} \\
|a - b| &= \sqrt{a^2 + b^2 - 2 a b} = \sqrt{r - 2 s}
\end{align}$$
so that
$$\{a,b\} = \frac{1}{2}\left(\sqrt{r + 2 s} \pm \sqrt{r - 2 s}\right)$$
Taking $a \ge b$, we eliminate the ambiguity:
$$
a = \frac{1}{2}\left(\sqrt{r+2s} + \sqrt{r-2s}\right) \qquad\qquad
b = \frac{1}{2}\left(\sqrt{r+2s} - \sqrt{r-2s}\right)$$
We can (and should) solve for $\theta$ and $\phi$. Start by observing ...
$$\begin{align}
p_x^2 + p_y^2 = a^2\cos^2\theta+b^2\sin^2\theta &\qquad
q_x^2 + q_y^2 = a^2\sin^2\theta+b^2\cos^2\theta \\
p_x^2 + q_x^2 = a^2\cos^2\phi + b^2\sin^2\phi &\qquad
p_y^2 + q_y^2 = a^2\sin^2\phi + b^2\cos^2\phi
\end{align}$$
so that
$$\begin{align}
\left(p_x^2+p_y^2\right)-\left(q_x^2+q_y^2\right) &= \left(a^2-b^2 \right)\left(\cos^2\theta-\sin^2\theta\right) = \sqrt{r^2 - 4 s^2}\;\cos 2\theta\\[6pt]
\left(p_x^2+q_x^2\right)-\left(p_y^2+q_y^2\right) &= \left(a^2-b^2 \right)\left(\cos^2\phi-\sin^2\phi\right) = \sqrt{r^2-4s^2}\;\cos 2\phi
\end{align}$$
whence
$$\cos 2\theta = \frac{\left(p_x^2+p_y^2\right)-\left(q_x^2+q_y^2\right)}{\sqrt{r^2-4s^2}} \qquad
\cos 2\phi = \frac{\left(p_x^2+q_x^2\right)-\left(p_y^2+q_y^2\right)}{\sqrt{r^2-4s^2}}$$
(Parameter $\theta$ itself isn't important for your purposes, but it's worth noting how its expression in terms of $P$ and $Q$ matches that of $\phi$.)