Test and simplify PyNutil methods

[sharoncy]

There are three methods: "all", "per_pixel" and "per_object".

To do: test them and check they produce correct results.

[sharoncy]

Method "All": Get results for pixel_count and object_count.
Method "per_pixel": Get results for pixel_count only
Method "per_object": Get results for object_count only.

[sharoncy]

Consider removing option to generate separate results for "per_pixel" and "per_object" (everything is covered by the "all" option). To do this remove all statements "if method in" something something "all" (these can be deleted as long as there isn't an "and" statement". e.g. line 311...).