Save worm features for use in Gepetto

[JimHokanson]

We are working on saving worm features (currently in the movement validation repo) into a format that Gepetto will work with.

The recording creator class is currently at: https://github.com/openworm/org.geppetto.recording/blob/master/org/geppetto/recording/GeppettoRecordingCreator.py

An example of using this is at: https://github.com/openworm/org.geppetto.recording/blob/master/org/geppetto/recording/CreateTestGeppettoRecording.py

Steps required: 1) Since we currently don't have the feature processing pipeline finished, we need to finish being able to load a MRC feature file from disk 2) When all the features are in memory, save them back into the new format (using code referenced above)

Code will be placed in: https://github.com/openworm/movement_validation/blob/master/movement_validation/features/worm_features.py

[JimHokanson]

@tarelli

How would the recording support matrices? Specifically the dimensions might be an issue.

Examples: Skeleton X: [frames,points_along_skeleton]: The second dimension represents points along the worm. X refers to the x dimension, we would also have Skeleton Y. Frames is the "time" dimension, i.e. every video frame.

More issues to come but I have to run ...

Jim

[JimHokanson]

@tarelli Additionally, is there any support currently for meta data? I am guessing there isn't. It might be nice to eventually add. Specifically, I'm thinking of a versioning system in case we update the file contents. It might be nice for the user to be able to see that the version # is different and then we could provide links to somewhere that explains what the differences are.

[slarson]

@JimHokanson @tarelli how's this one going?

[tarelli]

@slarson the linked issues provide the status for those two. Now @jrieke is looking at the recording format that is being developed at the Wojcik Lab and making sure it can handle these requirements too. Will update this as we make progress on that.

[MichaelCurrie]

I believe this is now handled by JSON_Serializer. If we make WormFeatures inherit from this class, then the save_to_JSON and load_from_JSON methods allow the worm features to be loaded and saved.

Linking this format to the recording creator class referenced above is something that might still need to be done, but the links in the first post on this issue are now broken. Can @tarelli or @JimHokanson give me an update? Thanks!

[slarson]

Should be moved to the appropriate geppetto repo. Closing for now.