Better angles from Hough

I decreased the size of the cells in the accumulator array that the Hough Transform uses and the accuracy of the angles of the detected lines significantly improved. Yesterday I was using a resolution of 1 radian, but now my resolution is pi/450.

There are still too many lines detected for the upper boxes compared to the lower boxes. Here is what I get when I plot the top 5 lines detected (instead of thresholding):

3 of the 5 lines detected are for the top horizontal line. The 12th line that is detected is the upper horizontal line for the PID. I'm not quite sure why that is. Here is what I get when taking the top 12 lines:


When I get greedy and increase the resolution of the angle too much, I start to hurt from it by failing to detect lines. For example, when I set the resolution to pi/720, my top 20 detected lines are the following:

It doesn't even detect the bottom horizontal line.

This is the process I've been using to detect the lines:
1. Resize the image to half of its size.
2. Take the gradient of the image.
3. Run edge.m on the vertical gradient image, specifying 'sobel' as a parameter.
4. Run the Hough Transform on the result of edge.m
5. Sort the accumulator matrix in descending order and plot the top x lines on top of the original image.

Here is an example vertical gradient of the image:

Here is an example of the output of edge.m, passed into the Hough Transform function:

Finally, here is an example of output from the Hough Transform function:

The white portions in the middle of the image correspond to the lines detected in the image.

The next significant problem is detecting the vertical lines. When I instead use the horizontal gradient, here are the top 20 lines I detect (none of which are useful):

Also, here is the output of the Hough Transform. Note how many white parts there are - meaning lots of lines were detected.

Ok one last thing - here is what is given to the Hough Transform function in the vertical case: