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The problem I'm having is I don't know what's the state of the art in Java Numerical libs, science packages and plotting libs. When I google I get a bewildering list of numerical packages, most of which turn out to have ceased development. With others it's not clear which scientific analysis packages share what underlying numerical libs (and thus would be interoperable). Thus I'm asking slashdot for advice.
I don't require the numerics package be native java (I'm willing to compile the libs for the native processor and use optimized array storage formats if there's more than a factor of 3 in performance boost and it's handled transparently in java). The arrays access should have an easy syntax that permits slicing and functions distributed over array elements in a manner reminiscent of matlab or numpy. I should be able to generate automatically sized and labeled 2 and 3-d plots of data easily without converting data types. And there should be a standard scientific library that includes things like fft, and non-linear solvers. Finally, I need either a non-commercial solution or one whose runtimes I can distribute freely, and it needs to be able to compile on linux and hopefully a mac too. I'd be willing to substitute R or Gnuplot graphics if I can easily call them from inside java without too much data format conversion. Any solution needs to be Groovy compatible or it defeats the purpose. Advice?"