Compute Head Direction Vector #276
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Thanks @b-peri! This is well implemented and well tested with the known values.
Some thoughts (apart from the things I point out in individual comments):
- would be nice to expand the tests a bit by checking for what happens if there is a NaN value. For example, you can make one of the ears NaN for a particular timepoint and test whether the head vector for that exact timepoint (and no other) is NaN.
- As we discussed today, you may move the new funciton to the kinematics module (anticipating our planned removal of the
analysislevel. - Once you compelete the above, it would be good to use this function within the polar vectors example. For that you'd need to modify the code to use your function for computing the head vector (instead of midpoint + snout) and update the plots accordingly. I think it's worth doing that in this PR, as that example will serve as the perfect documentation for the new feature. Btw, becasue the example scripts are broken down into cells (via
# %%), you can run them independently via ipython, which is helpful for debugging and editing that script. Let me know if you need help with that.
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sorry for the delay @b-peri !
From the longer discussion in zulip, I detail here what I think would be the simplest implementation.
I also added some comments about the tests, let me know if you have any questions. The basic idea is to split them based on their goals (e.g. split them if they test the error-catching, the behaviour with nans, or the 'ideal' behaviour) and parametrise them when possible.
Let me know if you'd like to discuss anything offline or if you have questions!
movement/analysis/kinematics.py
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| def compute_head_direction_vector( | |
| def compute_2D_head_direction_vector( |
or something of the like to make it clear that we are focusing on the top-down / bottom-up view case?
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Could this be more general than head direction?
It would work to compute any forward direction perpendicular to a line connecting two symmetrical points about the sagittal plane, right? For example, we could compute a forward vector that is always perpendicular to the line connecting both hips.
Maybe it's worth renaming?
Hey @b-peri , just a note to also remove any uppercase letters in function names. |
…_direction_vector()`
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Hi @lochhh, thanks for the heads-up, that's my bad! The function names are fixed now! |
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Description
This PR introduces the
navigationmodule and addscompute_head_direction_vector()- a function for calculating an animal's 2D head direction vector - tomovement. As described in #238, this function takes two keypoints (corresponding to the left and right of the head) and computes the vector perpendicular to the line connecting them, pointing in the animal's rostral direction.Since
compute_head_direction_vector()expects the input dataset to have specific dimensions (and specific keypoints), I've taken some notes from thekinematicsmodule here and added some validation to the beginning of the function. I expect that some of this will be factored out into a separate function as we continue to add to thenavigationmodule, but I've kept everything under the main function itself for the time being.What is this PR
References
Checklist: