Taylor, I asked Tom Malzbender about this topic. Let me speak for a moment about the photographic methodology and then I'll give you Tom's answer about how to get the the variable focus point. If I mis-remember the process, it may act as bait to bring Tom into the discussion.
In the simplest example, lets say you have a fixed camera pointing horizontally at the subject. The subject is on a translation stage, or its manual equivalent. A manual equivalent could be a square piece of plastic bounded on two sides by two horizontal rails so that the square plastic base could move closer or farther away from the camera. You would then determine the distance of the focal depth you require. For example, if your subject was half of a walnut shell and the distance between the bottom of the shell to the top of the shell facing the camera was 1 inch, your focal depth would be one inch. You would move the subject into the position where in the distant edge of the walnut shell would be in focus. You could then take 10 photographs with the subject translated away from the camera one 10th of an inch for each successive shot. as your subjects is translated backwards from the camera, different levels of the walnut shell will fall into the camera's depth of field “sweet spot”. Take care to align the the camera's optical axis, the direction passing through the center of the lens and striking the center of the sensor, with the axis of the subject's motion. Small shifts of the subject position due to minor misalignment can be eliminated using the forthcoming Alignment Tool from the CARE project with CHI and Princeton, written by Sema Berkiten.
I'll now give you Tom's answer. You will need to open a text editor to build a new type of LP file. On the 1st line writes the number 10. This indicates the number of images. On the next line, enters the absolute pathname for the image, which was shot when the subject was farthest from the camera (with the focus on the top of the walnut shell). following the pathname, hit the space bar or tab key, then enter 0.0. On the the next line, enter the absolute pathname for the next photo in the sequence, followed by a space or tab and then enter the value 0.1. Continue to increment the numerical value following each photo's absolute pathname to 0.2. 0.3, 0.4 and so on. The photo taken of the edge of the walnut shell, which was taken closest to the camera, would have the numerical value 0.9. So now you have a new type of LP file which uses one of the 2 available dimensions of the PTM, in this case depth. Tom said that you could also use the 2nd available dimension, for example, to translate the light along the x-axis. This is all I remember from Tom.
At this point, the rest of my answer is speculative because I have never actually built this kind of PTM. My best guess is that you would save your LP file Into the project's assembly files folder for RTIViewer or into the same directory as your images for the PTM fitter. I would then see what happens using this data in the RTIbuilder software and/or the command line HP PTM fitter. If either of these methods work, go ahead and try to view the PTM in RTIViewer or the PTMviewer.
Taylor, if you try this, PLEASE let us know what happens!