removed unused util code

keypoint_moseq/util.py

@@ -35,64 +35,6 @@ def interpolate_keypoints(keypoints, outliers, axis=1):
     return np.moveaxis(keypoints.reshape(init_shape),0,axis)
 
 
-
-'''
-def ppca(key, data, missing, num_components, num_iters=50, whiten=True):
-    batch_shape = data.shape[:-1]
-    data = data.reshape(-1, data.shape[-1])
-    missing = missing.reshape(-1, data.shape[-1])
-    N,D = data.shape
-    
-    observed = ~missing
-    total_missing = missing.sum()
-    means = masked_mean(data, observed)
-    stds = jnp.sqrt(masked_mean((data-means)**2, observed))
-    data = (data - means) / stds
-
-    # initial
-    C = jr.normal(key, (D, num_components))
-    X = data @ C @ jnp.linalg.inv(C.T@C)
-    recon = jnp.where(observed, X @ C.T, 0)
-    ss = ((recon - data)**2).sum() / (N*D-total_missing)
-
-    for itr in range(num_iters):
-        
-        # e-step
-        data = jnp.where(observed, data, [email protected])
-        Sx = jnp.linalg.inv(jnp.eye(num_components) + C.T@C/ss)
-        X = data @ C @ Sx / ss
-
-        # m-step
-        C = data.T @ X @ jnp.linalg.pinv(X.T@X + N*Sx)
-        recon = jnp.where(observed, [email protected], 0)
-        ss = (((recon-data)**2).sum() + N*(C.T@C*Sx).sum() + total_missing*ss)/(N*D)
-    
-    U = jnp.linalg.svd(C)[0]
-    C = U[:,:num_components]
-    vals, vecs = jnp.linalg.eigh(jnp.cov((data @ C).T))
-    order = jnp.flipud(jnp.argsort(vals))
-    vecs = vecs[:, order]
-    vals = vals[order]
-    C = C @ vecs
-    latents = (data*stds)@C
-    
-    if whiten:
-        Sigma = jnp.cov(latents.T)
-        L = jnp.linalg.cholesky(Sigma)
-        latents = jnp.linalg.solve(L, latents.T).T
-        C = jnp.linalg.solve(L, C.T).T
-    return C, means, latents.reshape(*batch_shape, num_components)
-
-
-def whiten(x):
-    shape,x = x.shape, x.reshape(-1,x.shape[-1])
-    mu = x[mask.flatten()>0].mean(0)
-    Sigma = jnp.cov(x[mask.flatten()>0].T)
-    L = jnp.linalg.cholesky(Sigma)
-    x = jnp.linalg.solve(L, (x-mu).T).T
-    return x.reshape(shape), L
-'''
-
 def center_embedding(k):
     return jnp.linalg.svd(jnp.eye(k) - jnp.ones((k,k))/k)[0][:,:-1]