Restructuring/Simplifying RunUseCase and associated utils to use Python API

[sheryjoe]

• flatten ellipsoid use case using shapeworks commands
• demonstrate step-by-step
• md documentation

e.g. shapeworks readeimage —name foo.nrrd bounding box —names *.nrrd crop write —name bar.nrrd

A - single image B- groupwise
Single command at a time
Multiple commands pipped (save alot on io)

1. isoresample
 2. pad
 3. com alignment (center of mass)
 4. extract label
 5. close holes
 6. compute dt (distance transform)
 7. threshold (probably binarize, but can be "label")
 8. rigid alignment
 a. tp smooth (topology preserving)
 b. icp (iterative closest point) registration
 9. bounding box
 10. cropping
 Now we have aligned, binarized, cropped images.


Goal 2: Mesh it (?)
 1. mesh from dt (distance transform)
 2. ...???


Goal 3: Optimize?


Goal 4: Analyze?
 ??

[sheryjoe]

This will be feasible once python APIs are exposed in use cases. pushing this to 5.6

[sheryjoe]

Closing this. Replaced by #865

[sheryjoe]

Related to #818