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So what's the best way currently. Going through ipython console. Also, just save the affine or use something like pybdv to save both layers and their affine transforms?
Currently I've only ever played with it so haven't saved anything. But yes, going through the console will get you there for now.
My current plan was to add an output folder selection widget, and have the affine matrix saved as ref-layer-name--moving-layer-name--affine.txt or something similar. Alternative suggestions are most welcome!
Currently there's no built-in way to save the found affine transforms. We should find a way to set saving options within the plugin.
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