The Judge said no to the Defense. Think of it this way. Remember the old man FBI guy that talked about the cell phones? Pros objected that Defense wanted to ask about an email that explained some software. Pros said that the witness didn't have that email so Defense should not be able to question him (this was before we foundout witness did have it, but that doesn't hurt my initial example). Anyhow, the Pros said because the witness hadn't seen that exact email and had discussion on it then he would not be able to comment on it. Now the Pros is saying, you can run your own, yes, it will be different data output, but you can question the witness on that. The Pros wants both sides of the fence, and then muddies it up more by bringing in National Security as to why the Defense could not look at what the Pros is saying is evidence against him.
Do you see the disconnect? How can Defense question the witness on something that has a different data output if they run their own when he needs to ask witness about the data that the witness found when he ran his report? It makes no sense.
Defense did not want the process or procedure, he jsut wanted the final output so he could see what was being used as evidence so he could question it.