imagej/imagej-legacy — pull request #59 by dscho (2014-06-17 16:40:38+00:00)
Title: Fix run('Some Macro', 'macro options');

Aryeh Weiss reported that macros that are registered menu items (by putting them into `Fiji.app/plugins/*_*.ijm`) ignore the macro options passed via `IJ.run`'s second parameter.

The reason is that ImageJ 1.x insists on making the macro options thread-local (which does not address the threading issues with running macros completely because there is too much global state going on in ImageJ 1.x for that, but that is beside the current issue) and SciJava's `ScriptService` runs scripts in a separate thread pool.

The solution is to remember the options and set them thread-locally just before running the macro from the ImageJ 1.x macro engine.

This requires scijava/scijava-common#85 to be merged first.

This branch also fixes a couple of other bugs identified while implementing a regression test to verify that the original issue has been solved.