Finish colocalization

[etadobson]

• [x] merge Colocalize command for global methods
• [x] finish SACA code (see below comment)
• [x] wrap SACA code in Ops
• [x] add SACA Op to Colocalize command
• [ ] MTKT needs some TLC !!! (see issue #619)
• [ ] send to Ming/Shulei for maths tests
• [ ] contact Nate Sherer for bio-dataset testing
• [ ] announce!

[etadobson]

• [x] make Shulei's java implementation stable (ie - use random(seed))
• [x] add a unit test validating behavior of the algorithm (using small synthetic double[][]'s as input)
• [x] propagate random(seed) update to Imglib2 version (make sure unit tests still pass)
• [x] code style / clean-up pass (no public fields, minimal public API, non-public helper classes...)
• [x] consider getting rid of OO design (constructor/execute... in favor of static method) (have static method that takes same arguments as constructor and pass to execute())
• [x] address new performance bottlenecks...
• [x] ensure better Random behavior... don't create a new one with each call to WtKendallTau
• [x] convert to Ops computer style where result image is preallocated and passed to the algorithm
• [x] image creation factory needs to support creating buffers of a different type... RAI<T> to RAI<U> and result should be RAI<V> ... should use input image type <I>, intermediate type <T>, and output type <O>
  • [x] when testing, make sure to pass factory that produces DoubleType images always for consistency with Shulei's original code
• [x] contact Shulei... ask if other outputs should be made available to users (ie - double-check p-values / confidence scores / threshold cutoffs)
• [x] noticed intermediate and result NaNs - why?

[etadobson]

https://github.com/imglib/imglib2/pull/273

[etadobson]

The output from the SACA op needs to be signed!!! "The pixel-wise z-score output from SACA not only reflects colocalization or anti-colocalization at each pixel by its sign, but also shows the degree of colocalization or anti-colocalization through its absolute values."