scifio/scifio — pull request #67 by hinerm (2013-09-27 18:26:43+00:00)
Title: No more dim order

This patch refactors the SCIFIO API to be N-dimensional, instead of the 5-D model currently used by Bio-Formats.

NB: these changes are not ready to be merged, as the history needs to be cleaned up (at a minimum).

However, this work is at the point where all the maven tests are passing.

I will start to test with IJ2 and fix any associated bugs, but I wanted to open this up to review now in case there are objections to any significant portions of code.

Personally I would like to find a way to simplify some of the actual N-dimensional reading code (ImgOpener, AbstractArrayLoader, FakeFormat). In each case I implemented a recursive read method to handle the arbitrary number of planes and planar dimensions. This code is fairly complicated and may not be easy to understand/troubleshoot. If anyone has input on how to consolidate or simplify this that'd be great. (I haven't actually tried to do so myself yet, as I focused on getting tests passing first)