I think dynamic programming might be your friend.
The first step I see is to divide the polyhedron into a trivial collection of blocks such that every possible face is available (i.e. slice and dice it into the smallest pieces possible). This should be trivial because everything is an axis aligned box, so k-tree like solutions should be sufficient.
This seems reasonable because I can look at its cost. The cost of doing this is that I "forget" the original configuration of hyperslabs, choosing to replace it with a new set of hyperslabs. The only way this could lead me astray is if the original configuration had something to offer for the solution. Given that you want an "optimal" solution for all configurations, we have to assume that the original structure isn't very helpful. I don't know if it can be proven that this original information is useless, but I'm going to make that assumption in this answer.
The problem has now been reduced to a graph problem similar to a constrained spanning forest problem. I think the most natural way to view the problem is to think of it as a graph coloring problem (as long as you can avoid confusing it with the more famous graph coloring problem of trying to color a map without two states of the same color sharing a border). I have a graph of nodes (small blocks), each of which I wish to assign a color (which will eventually be the "hyperslab" which covers that block). I have the constraint that I must assign colors in hyperslab shapes.
Now a key observation is that not all possibilities must be considered. Take the final colored graph we want to see. We can partition this graph in any way we please by breaking any hyperslab which crosses the partition into two pieces. However, not every partition is meaningful. The only partitions that make sense are axis aligned cuts, which always break a hyperslab into two hyperslabs (as opposed to any more complicated shape which could occur if the cut was not axis aligned).
Now this cut is the reverse of the problem we're really trying to solve. That cutting is actually the thing we did in the first step. While we want to find the optimal merging algorithm, undoing those cuts. However, this shows a key feature we will use in dynamic programming: the only features that matter for merging are on the exposed surface of a cut. Once we find the optimal way of forming the central region, it generally doesn't play a part in the algorithm.
So let's start by building a collection of hyperslab-spaces, which can define not just a plain hyperslab, but any configuration of hyperslabs such as those with holes. Each hyperslab-space records:
- The number of leaf hyperslabs contained within it (this is the number we are eventually going to try to minimize)
- The internal configuration of hyperslabs.
- A map of the surface of the hyperslab-space, which can be used for merging.
We then define a "merge" rule to turn two or more adjacent hyperslab-spaces into one:
- Hyperslab-spaces may only be combined into new hyperslab-spaces (so you need to combine enough pieces to create a new hyperslab, not some more exotic shape)
- Merges are done simply by comparing the surfaces. If there are features with matching dimensionalities, they are merged (because it is trivial to show that, if the features match, it is always better to merge hyperslabs than not to)
Now this is enough to solve the problem with brute force. The solution will be NP-complete for certain. However, we can add an additional rule which will drop this cost dramatically: "One hyperslab-space is deemed 'better' than another if they cover the same space, and have exactly the same features on their surface. In this case, the one with fewer hyperslabs inside it is the better choice."
Now the idea here is that, early on in the algorithm, you will have to keep track of all sorts of combinations, just in case they are the most useful. However, as the merging algorithm makes things bigger and bigger, it will become less likely that internal details will be exposed on the surface of the hyperslab-space. Consider
+===+===+===+---+---+---+---+
| : : A | X : : : :
+---+---+---+---+---+---+---+
| : : B | Y : : : :
+---+---+---+---+---+---+---+
| : : | : : : :
+===+===+===+ +---+---+---+
Take a look at the left side box, which I have taken the liberty of marking in stronger lines. When it comes to merging boxes with the rest of the world, the AB:XY surface is all that matters. As such, there are only a handful of merge patterns which can occur at this surface
- No merges possible
- A:X allows merging, but B:Y does not
- B:Y allows merging, but A:X does not
- Both A:X and B:Y allow merging (two independent merges)
- We can merge a larger square, AB:XY
There are many ways to cover the 3x3 square (at least a few dozen). However, we only need to remember the best way to achieve each of those merge processes. Thus once we reach this point in the dynamic programming, we can forget about all of the other combinations that can occur, and only focus on the best way to achieve each set of surface features.
In fact, this sets up the problem for an easy greedy algorithm which explores whichever merges provide the best promise for decreasing the number of hyperslabs, always remembering the best way to achieve a given set of surface features. When the algorithm is done merging, whatever that final hyperslab-space contains is the optimal layout.
I don't know if it is provable, but my gut instinct thinks that this will be an O(n^d) algorithm where d is the number of dimensions. I think the worst case solution for this would be a collection of hyperslabs which, when put together, forms one big hyperslab. In this case, I believe the algorithm will eventually work its way into the reverse of a k-tree algorithm. Again, no proof is given... it's just my gut instinct.
