search

openworm / open-worm-analysis-toolbox

A testing pipeline that allows us to run a behavioural phenotyping of our virtual worm running the same test statistics the Schafer Lab used on their worm data.
Other
48 stars 27 forks source link

Foraging Amplitude Units #206

Open MichaelCurrie opened 7 years ago

MichaelCurrie commented 7 years ago

From @ver228

A quick question. I am documenting the features however I found in this document ( https://github.com/openworm/open-worm-analysis-toolbox/blob/master/documentation/database%20schema/Features%20Specifications.xlsx) that locomotion.foraging_bends.amplitude should have units of micrometers.

However, for what i understand from the code the foraging_bends.amplitude is the maxima of the nose angles within a time window (https://github.com/openworm/open-worm-analysis-toolbox/blob/master/open_worm_analysis_toolbox/features/locomotion_bends.py#L679), so it should have units of degrees.

I think the units might be wrong in the original paper. From the Supplementary Material "The foraging amplitude is defined as the largest foraging angle measured, prior to crossing 0°", and because it is an angle it clearly should have units of degrees, but then in Supplementary Table 2 the corresponding features do have units of Microns.

MichaelCurrie commented 7 years ago

@ver228 from everything you say it certainly makes sense that it should be degrees. I wonder if we should seek clarification from @Eviatar.

Eviatar commented 7 years ago

Yep, my mistake. We discovered this a few days ago. I've been working with Andre & Avelino to help move the code forward. There are a few things on the list & the goal is to take care of them just after the UCLA worm meeting this coming week.

MichaelCurrie commented 7 years ago

OK thanks @Eviatar, see you there btw! WCON's poster session is Thursday 22 June from 21:00 to 22:30.

Eviatar commented 7 years ago

Awesome, looking forward to it!