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I am trying to understand how to use, what it requires compute the homogenous transformation matrix.

I know 2 points from 2 different frames, and 2 origins from their corresponding frames.

I how transformation matrix looks like, but whats confusing me is how i should compute the (3x1) position vector which the matrix needs. As i understand is, this vector a origin of the old frame compared to the new frame. But how to calculate it, the obvious answer (I think) would be to subtract both ($O_{new} - O_{old}$ ), but it does not feel right.

I know its a simple question but my head cannot get around this issue, and how can i prove it the right way, with the information i know?

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A homogeneous transformation matrix $H$ is often used as a matrix to perform transformations from one frame to another frame, expressed in the former frame. The translation vector thus includes [x,y(,z)] coordinates of the latter frame expressed in the former. Perhaps that this already answers your question, but below is a more elaborate explanation.

The transformation matrix contains information about both rotation and translation and belongs to the special Eucledian group $SE(n)$ in $n$-D. It consists of a rotation matrix $R$ and translation vector $r$. If we permit no shear, the rotation matrix contains only information about the rotation and belongs to the orthonormal group $SO(n)$. We have:

$$H=\begin{bmatrix} R & r \\ \bar{0} & 1 \end{bmatrix}$$

Let's define $H^a_b$ the transformation matrix that expresses coordinate frame $\Phi_b$ in $\Phi_a$, expressed in $\Phi_a$. $\Phi_a$ can be your origin, but it can also be an other frame.

You can use the transformation matrix to express a point $p=[p_x\ p_y]^\top$ (vectors) in another frame: $$P_a = H^a_b\,P_b$$ $$P_b = H^b_c\,P_c$$ with $$P = \begin{bmatrix} p \\ 1 \end{bmatrix}$$ The best part is that you can stack them as follows: $$P_a = H^a_b H^b_c\,P_c = H^a_c\,P_c $$ Here a small 2 D example. Consider a frame $\Phi_b$ translated $[3\ 2]^\top$ and rotated $90^\circ$ degrees with respect to $\Phi_a$. $$H^a_b = \begin{bmatrix}\cos(90^\circ) & -\sin(90^\circ) & 3 \\ \sin(90^\circ) & \cos(90^\circ) & 2 \\ 0 & 0 & 1 \end{bmatrix}=\begin{bmatrix}0 & -1 & 3 \\ 1 & 0 & 2 \\ 0 & 0 & 1 \end{bmatrix}$$ A point $p_b=[3\ 4]^\top$ expressed in frame $\Phi_b$ is $$\begin{bmatrix}p_{a,x} \\ p_{a,y} \\ 1 \end{bmatrix} = \begin{bmatrix}0 & -1 & 3 \\ 1 & 0 & 2 \\ 0 & 0 & 1 \end{bmatrix}\begin{bmatrix}3 \\ 4 \\ 1 \end{bmatrix}=\begin{bmatrix}-1 \\5 \\1 \end{bmatrix} \to p_a = \begin{bmatrix}-1\\5\end{bmatrix}$$ Try to make a drawing to improve your understanding.

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