Config: Replace Ini With Yaml

Contents:

• Replace ini with yaml discussion
• Provide support for and automated transform between yaml and json

Replace ini with yaml

See Cmiclab issue #189. Below is a summary. Yaml is a good candidate format because it supports nesting but is very terse and human readable. Json was considered as a format, but the majority opinion was against it due to the need to close nesting. See the next section for a potential resolution to that, however. Protobuf was also considered but no implementation appears to have been done.

The branch for this work on github is 168-migrate-configuration-files-to-yaml.

Automatic support of json and yaml through config code

There isn't really a strong reason why we can't support json, given support for yaml. They both have parsers that convert between a file and a python dictionary, so whatever we choose to support in terms of yaml nesting should also be expressible in json. Json configs would be useful in the case that niftynet is being run in inference mode and takes json arguments from the query, potentially