Investigate generating Slicer CLI definitions from DIPY workflows

[ebrahimebrahim]

SlicerDIPY

I'm not aware of any such extension. But I don't see anything tricky in the dipy package dependencies so it should be straightforward to run it in the Slicer Python environment.

some standardized interface [...] convert all into individual slicer CLI modules

The Slicer CLI modules are just declared with an xml file that declares input and output arguments.

It looks to me like there is some way to build off of IntrospectiveArgumentParser and cli_flows to grab the input/output arguments and export appropriate xml for each one. I don't exactly know the details, but it assembles an argparse parser so all the information must be there one way or another.

Doing this will drop any caching/chaining support, though, since the Slicer CLI runner saves nodes to temp directory and runs the CLI on those files. There may be some way to specify metadata out of band but I suspect that'll clobber any caching mechanisms.

https://github.com/dipy/dipy/blob/master/dipy/workflows/base.py

https://github.com/dipy/dipy/blob/master/dipy/workflows/cli.py

[ebrahimebrahim]

I think must be the "SlicerDIPY" that I was remembering/hallucinating earlier: https://www.na-mic.org/wiki/2017_Winter_Project_Week/DiPy_in_Slicer

And I couldn't find much on the Slicer discourse.

So it seems there isn't much already done in this space.