Region Mapping when subcortical regions are present

Bugs related to region mapping being incomplete (i.e. not including the subcortical regions) are present in the scientific library of tvb.

What I could detect so far are the following:

• Region mapping defined in sim.stimulus.configure_space() method of Simulator class doesn't include the subcortical regions. This has been recently resolved.
• Spatial mask of the SpatialAverage monitor doesn't take into account the subcortical regions. A solution is in progress.
• In the Simulator class, definitions of Region Mapping are present in multiple ways, such as sim._regmap or sim.surface.region_mapping. Is this a good way to do it?

A solution would be to directly implement in the RegionMapping class, a method called full_region_mapping() that would return a mapping for all the available regions in the connectivity matrix, both for cortical and sub-cortical regions. For this the connectivity matrix and the surface (Cortex) data will be given in argument.

The instances where region mapping is used are being studied, focusing on the Simulator class first, but also on the classes related to it in the code, and using the full_region_mapping() method to provide a single region mapping solution for all current case scenarios.

Updates:

• The Region_Mapping.full_region_mapping(surf, conn) only returns a numpy array, since this is how _regmap is used.
• The Cortex uses a region_mapping_data that only uses the RegionMapping.from_file() method and that only includes the cortical regions, this should change.
• A single region_mapping should be used that always includes the cortical and sub-cortical regions.