First pass at improving test coverage
- Added test for recently introduced functionalities:
PeakFinder2D,ImageGradient, masks and indexing a single frame. - Added some missing logging of core modules
- Removed some old tests that either did things that were already covered, or did nothing
- Migrated some python tests to C++
Fixes #544 (closed), #545 (closed), #574 (closed), #550 (closed),