Faster

I've heard from the company that manufactures our DM and WFS that they can achieve frame rates an order of magnitude higher than what I'm capable of doing, around 800 Hz. This blows my mind since I have no idea how I make any more than incremental improvements with the Matlab commands I'm using now. In a sense this pisses me off since I'm not sure how we would have found this out if my advisor hadn't brought it up. It seems common in this industry for companies to ignore what most people are doing and write their own, barely adequate, proprietary software, and then go into stealth mode with the support.

Anyway, we're focusing on the DM first since that's most likely the harder problem. I'm actually skeptical they can get the frame rates they claim, but who knows. I've sent them the code I'm current using-code that was adapted from stuff they sent us-so I should hear something soon. I fully expect to hear complaints about a variety of minor coding transgressions and other shit that doesn't matter.

Nonetheless, I'm assuming that I can eventually speed things up significantly on the hardware side, which means that my software will have to change as well. Right now the most significant software bottleneck is the script for calculating the slope vector from the WFS image. For a full frame 1280x1024 Hartmann image, calculating the slopes in Matlab takes around 0.08 seconds for a grid of around 40x40 lenselets. The problem, as I mentioned before, is that finding the centroids is not a linear operation since you have to divide by the sub-aperature intensity, thus you can't just multiply the image by some matrix. Loops in Matlab are shit, so looping over all the sub-aperatures is what causes most of the delay.

Right now I'd like to try to reduce the computation time in Matlab by reducing the centroid calculation to 2 linear operations on the image. if I is the vectorized image, then there is a (sparse, large) matrix A such that S1 = A*I, where S1 is a vector of unnormalized slopes. There is also another matrix Q such that L = Q*I where L contains the total intensity in each sub-aperature. The slope vector is then (in Matlab speak) S = S1./[L;L] (since S1 contains x and y slopes).

I have no idea if this is really faster, but there's enough evidence to give it a try. Coming up with A efficiently though isn't easy, but hopetully I'll finish that tomorrow.