Fusing 2D orientations to 3D¶

Flydra uses an extended Kalman filter (EKF) and a simple data association algorithm to fuse 2D orientation data into an a 3D orientation estimate. The program flydra_analysis_orientation_ekf_fitter is used to perform this step, and takes, amongst other data, the 2D orientation data stored in the slope column of the data2d_distorted table and converts it into the hz_line* columns of the ML_estimates table. (The directional component of these Pluecker coordinates should be ignored, as it is meaningless.)

See smoothing orientations for a description of the step that chooses orientations (and thus removes the 180 degree ambiguity in the body orientation estimates).

The following sections detail the algorithm used for the finding of the hz_line data.

Process model¶

We are using a quaternion-based Extended Kalman Filter to track body orientation and angular rate in 3D.

From (Marins, Yun, Bachmann, McGhee, and Zyda, 2001) we have state where are angular rates and are quaternion components (with the scalar component being ).

The temporal derivative of is and is defined as:

The process update equation (for ) is:

Where is the noise term with covariance and is the time step.

Observation model¶

The goal is to model how the target orientation given by quaternion results in a line on the image, and finally, the angle of that line on the image. We also need to know the target 3D location, the vector , and the camera matrix . Thus, the goal is to define the function .

Quaternion may be used to rotate the vector using the matrix R:

Thus, for the default, non-rotated orientation, we find , the orientation estimate.

Now, considering a point passing through with orientation given by , we define a second point .

Given the camera matrix :

The image of point is . Thus the vec on the image is .

Now, we need to shift coordinate system such that angles will be small and thus reasonably approximated by normal distributions. We thus take an expected orientation quaternion and find the expected image angle for that :

We define our new observation model in this coordinate system:

Of course, if the original observation was , the new observation must also be placed in this coordinate system.

The EKF prior estimate of orientation is used as the expected orientation , although is possible to use other values for expected orientation.

Data association¶

The data association follows a very simple rule. An observation is used if and only if this value is close to the expected value. Due to the definition of above, this is equivalent to saying only small absolute values of are associated with the target. This gating is established by the --gate-angle-threshold-degrees parameter to flydra_analysis_orientation_ekf_fitter. --gate-angle-threshold-degrees is defined between 0 and 180. The basic idea is that the program has a prior estimate of orientation and angular velocity from past frames, and any new 2D orientation is accepted or not (gated) based on whether the acceptance makes sense – whether it’s close to the predicted value. So a value of zero means reject everything and 180 means accept everything. 10 means that you believe your prior estimates and only accept close observations, where as 170 means you think the prior is less reliable than the observation. (IIRC, the presence or absence of the green line in the videos indicates whether the 2D orientation was gated in or out, respectively.)

--area-threshold-for-orientation lets you discard a point if the area of the 2D detection is too low. Many spurious detections often have really low area, so this is a good way to get rid of them. However, the default of this value is zero, so I think when I wrote the program I found it to be unnecessary.