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If you can stick with Java, then I would recomend it. Because then the nice guys from OpenCV have already saved you the work of setting up JNI and the JNI wrapper.
Debugging for your PC is much, much more convenient than debugging for native Android NDK code! So if you want to use the NDK (because of reasons rwong already mentioned), I would highly recommend to develop a desktop wrapper for your computer vision code so that you can run it both on Android and your PC. (Pro tip: this keeps your code modular).
