Directionality for ROIs

[bancroftg]

Unable to determine directionality (in respect to ROIs):

When I go to "Aggregate Boolean Conditional Statistics" I do not have any conditional rule behavior options "facing" the ROIs, only options where the animal is "in zone". This is after successfully drawing ROIs, analyzing ROI data aggregates, and extracting features. After extracting features, I appended ROI features by body part.

When I initially created this project, I did not use a SimBA suggested animal body-part config, but instead produced my own. It is 4 points with a center point instead of the tail. Am I required to use a SimBA body-part config in order to compute directionality?

Please let me know and thank you!

[sronilsson]

Hi @bancroftg!

In order to compute where the animal is facing in relation to ROIs and other animals in SimBA GUI, it requires body-parts for the left ear, nose, and right ear. It's done like the image below.

However, if SimBA cannot find a body part name that contains the two words left and ear, and another body part containing the two words right and ear, and a third body-part with the word nose, it doesn't know which body-part is which and direction/facing will not be computed.

What are the names of your 4 body-parts you are tracking and what body-parts are they? (PS. its possible to use the nape of the neck as well if you don't have the ears tracked but it would have to be done programmatically and not in GUI.

[bancroftg]

I have left ear, right ear, nose, and center. When I append the features do they need to be in any specific order?

[sronilsson]

No, no specific order required - can you send me an example CSV file from the project_folder/csv/features_extracted directory?

Do you know if you have columns in those files with the _facing suffix?

[bancroftg]

5218_dSLR_test_A1.csv

Not seeing _facing suffux

[sronilsson]

Cheers, let me check the code to remind myself what could be happening.

[sronilsson]

Ah yeah I can see.. you use a space in the bodypart name, while the code tries to split the bodypart name exlusively by _ .... so left_ear or ear_left works while ear left or left ear doesn't work. Let me improve that code.

[bancroftg]

Thank you!

[sronilsson]

I inserted a fix that also works on your body-parts as you named them. Just got to take the dog for her walk she is growling at me lol, I will push the update when I get back and let you know.

[sronilsson]

If you update Simba with pip install simba-uw-tf-dev upgrade, how does it look on your end if you try to run the ROI feature extraction again followed by the conditional booleans?

[bancroftg]

I ran the Simba update as pip install simba-uw-tf-dev --upgrade and ran feature extraction again. This gave me the directionality info perfectly! Thank you!

[sronilsson]

@bancroftg cool - one question: I just ran this boolean conditional analysis, and it just outputted a single aggregate count of when the behaviors happened (or not happened) at the same time. I didn't get any values for the exact time period bouts when they happened at the same time. Do you think that would be useful to add?

[bancroftg]

Oh Definitely! And the features extracted csv's give a frame-by-frame analysis, correct?

[bancroftg]

I have another small issue actually: When I now go to "Visualize ROI features" with the following settings, I'm running into an error:

[sronilsson]

Ah yeah, let me fix that too - while I do: how does it look if you tick the Multi-process checkbox, doe sit run then?