advanced_numpy: Fixed a bug in the function dot_product_partially_normalized where broadcasting was not happening as expected. Also, tweaked some doctests that failed silently. Added doctests to catch this case.
advanced_image_processing: Change the function merge_neuron_sets so that it uses distances between neurons and masks calculated by separate tested functions as a part of further testing and refactoring.
HDF5_logger: Made sure all overwrite options were False by default. Also, added a few lines to make sure a group is deleted whether or not debugging occurs. Lastly, made sure that a group is used whether or not it is overwritten as long as it exists. If it doesn't exists, the group is created and used.
batch_learner: Changed call to HDF5_logger.generate_HDF5_array_debug_logger force overwrite_group.
advanced_image_processing: Changed array_debug_logger_enumerator to create a new group to place all the intermediate results from processing each dictionary image.

This commit marks the successful completion of a few outstanding items. Though the fixes occurred in earlier commits, other changes surrounding them did not make them fully stable or nicely testable. Except for the fact that vigranumpy cannot get local maxima on edges, which we don't want anyways, we have found the missing local maxima on plateaus meaning #15 is fixed. Also, after fixing the distance measurement and tweaking parameters, we have found the missing neurons. The distance measurements have been separated into nice doctested functions that are now used, which aids in further refactoring and building tests for the code. In short, this means #14 is fixed. Testing and refactoring are not complete, but good progress has been made in this direction. In particular, more work has occurred in addressing any lingering concerns regarding #2. In short, many challenging issues have been resolved. Now, focus will be placed on further testing and integration concerns.