Improve menu functionality

[ctrueden]

From Ann Wheeler:

menu functionality e.g. selecting what to colocalise and which coefficients are needed. This is implemented in colocalisation threshold (set options checkbox), though this is mathematically weaker than Coloc2 and colocalisation threshold can't colocalise ROIs from the ROI manager.

Migrated-From: http://fiji.sc/bugzilla/show_bug.cgi?id=1100

[chalkie666]

we need to design and implement the "real" GUI.... taking lessons from jacop's GUI in the process, and getting "voice of user" input to make sure we deliver something that meets folks needs generally.
There are a lot of algorithms to choose from already, and more may well come, so it could get messy very quickly.

[chalkie666]

see issue #27

[chalkie666]

i suggest running all algorithms that are user selected, then since each algorithm may well produce several results values...out put all of those for each algorithm. You might not know which kinds of results are the ones which you want beforehand.... Further, handling so many different results to choose from in the input GUI would get too messy.
Rather, at results saving time there could be a checkbox list or something to choose which ones exactly to save, but by default save everything. But i am weary of even this, as it adds complecity that the user can deal with in the next step quite easily in R or a spread sheet with minimal effort.

When using macros, this would be hard to expose in a macro command line... as there would be far too many parameters.... there already are... so just default to writing out all possible computed results, and let the user process the ones they want downstream in R or knime or whatever.