This repo contains code to run an Ensemble Kalman Smoother (EKS) for improving pose estimation outputs.
First you'll have to install the git
package in order to access the code on github.
Follow the directions here
for your specific OS.
Then, in the command line, navigate to where you'd like to install the eks
package and move
into that directory:
$: git clone https://github.com/colehurwitz/eks
$: cd eks
Install the requirements:
$: pip install -r requirements.txt
To make the package modules visible to the python interpreter, locally run pip
install from inside the main eks
directory:
$: pip install -e .
We provide several example datasets and fitting scripts to illustrate use of the package.
The singlecam_example.py
script demonstrates how to run the EKS code for standard single-camera
setups.
Any of the provided datasets are compatible with this script; below we'll use data/ibl-pupil
as
our example.
To run the EKS on the example data, execute the following command from inside this repo:
python scripts/singlecam_example.py --csv-dir ./data/ibl-pupil --bodypart-list pupil_top_r pupil_bottom_r pupil_left_r pupil_right_r
The multicam_example.py
script demonstrates how to run the EKS code for multi-camera
setups where the pose predictions for a given model are all stored in a single csv file.
For example, if there is a body part names nose_tip
and three cameras named
top
, bottom
, and side
, then the csv file should have columns named
nose_tip_top
, nose_tip_bottom
, and nose_tip_side
.
We provide example data in the data/mirror-mouse
directory inside this repo,
for a two-view video of a mouse with cameras named top
and bot
.
To run the EKS on the example data provided, execute the following command from inside this repo:
python scripts/multicam_example.py --csv-dir ./data/mirror-mouse --bodypart-list paw1LH paw2LF paw3RF paw4RH --camera-names top bot
The pupil_example.py
script requires a csv-dir
which contains lightning-pose or DLC
model predictions.
To run this script on the example data provided, execute the following command from inside this repo:
python scripts/pupil_example.py --csv-dir ./data/ibl-pupil
The multiview_paw_example.py
script requires a csv-dir
which contains lightning-pose
or DLC model predictions for the left and right camera views, as well as timestamp files to align
the two cameras.
To run this script on the example data provided, execute the following command from inside this repo:
python scripts/multiview_paw_example.py --csv-dir ./data/ibl-paw
Cole Hurwitz
Matt Whiteway