Add extra image_set options

[derollins]

Is your feature request related to a problem? Please describe. There is a growing number of output files generated at various stages, these images take time to generate and also increase the storage taken up by the output files.

Describe the solution you'd like Add extra flags to the image_set maybe --image for just the flattened image, --masks for masked images, --traces for image trace overlays.

Cropped images could be turned on and off separately if grain stats are turned on.