The --cleanup parameter

[jeffctaylor]

While I generally like programs to be able to run with minimal interaction from the user (preferably none, actually, after the command line parameters have been set), I think the --cleanup parameter should probably ask for confirmation from the user. It only removes certain subdirectories under the images directory specified by the user, but this is still something that can be run by accident, so maybe we should say something like:

The following directories will be removed:
./image_data/registered
./image_data/convolved
./image_data/resampled
Do you wish to proceed (y/n)?

Just as a way of helping to prevent any "oops, wait!" moments.

[sophiathl]

That sounds very thoughtful - I remember some quite many "oops, wait!" moments of mine!