Merging morphounit and NeuronUnit's morphology.py

[rgerkin]

@appukuttan-shailesh @pedroernesto
@JustasB from my lab put together some morphology tests of his own here, which have many similarities to yours. His are based on the original L-Measure, and the accompanying python package pyLMeasure.

Can we discuss possibly merging this and morphounit?

[pedroernesto]

For now, what I see is that some features being tested by means of pyLMeasure maybe do not exist in NeuroM, which is the API we use in MorphoUnit. So, both lines of work may complement each other. I would suggest to discuss this issue with Andrew probably next week, when he is back.

Btw, I have to upload my last work on morphounit to this original repository, which I did on March-April following a Sailesh's hint, with the aim to keep MorphoUnit more generic. The work is in my forked repository: https://github.com/pedroernesto/morphounit

The most recent improvements can be summarized as follows:

• Checks the compliance of the raw observation file with NeuroM's (fst module) nomenclature.
• Automatic creation of configuration files for morph_stats and NeuroM, from that raw observation file.
• Deletes some neurite's morphometrics added by morph_stats, but not present in the observation file.
• Reversed to plural the number in feature names generated by morph_stats in the prediction file, to make it compatible with the observation file.
• Added more features that can be specified in the observation file. They can now be generated in the prediction file by means of other NeuroM modules than morph_stats, e.g. field diameter, bounding-box -X,Y,Z- extents and -largest,shortest- principal extents

[appukuttan-shailesh]

Interesting to see this as just yesterday I was updating the MorphoUnit usecase.

@rgerkin : For sure it would be nice to have them merged into a single package. We could maybe take this up during our next video call (Monday, 29th July)?

@pedroernesto : Yesterday I had made a pull request to merge your most recent changes into the repo and have a new release (for employing in the usecase). I intend to get it done today.

[rgerkin]

Sounds good. We'll discuss this at the 7/29 meeting.

[rgerkin]

I added this to the Slack message from several months ago (which I missed until now), but the full list of L-measure features is shown here in the left-hand column.