124 apps as modules

[stian-johnsen]

Status

Testing

Description

This PR covers the changes proposed in tickets #346 and #124. It introduces a module wrapper allowing for the running of NiftyNet applications in 3rd-party code, and a set of changes that enable the input from and output to memory of images.
The code is known to work for segmentation and regression applications. However, the changes made to the GAN, classification, and registration applications have not been tested.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• My code follows the code style of this project.
• I have added tests to cover my changes.
• All new and existing tests passed.

Impacted Areas in Application

List general components of the application that this PR will affect:

• niftynet.io.*
• niftynet.application.*
• niftynet.layer (preprocessing layers)
• demos

[ericspod]

This has to be left to last as it involves a lot of file changes. Other PRs and issues must be resolved first.