Updated use of weights in procrustes analysis.

trimesh/registration.py

@@ -209,10 +209,8 @@ def procrustes(
     Finds the transformation T mapping a to b which minimizes the
     square sum distances between Ta and b, also called the cost.
 
-    Optionally specify different weights for the points in a to minimize
-    the weighted square sum distances between Ta and b, which can
-    improve transformation robustness on noisy data if the points'
-    probability distribution is known.
+    Optionally filter the points in a and b via a binary weights array.
+    Non-uniform weights are also supported, but won't yield the optimal rotation.
 
     Parameters
     ----------
@@ -221,7 +219,11 @@ def procrustes(
     b : (n,3) float
       List of points in space
     weights : (n,) float
-      List of floats representing how much weight is assigned to each point of a
+      List of floats representing how much weight is assigned to each point.
+      Binary entries can be used to filter the arrays; normalization is not required.
+      Translation and scaling are adjusted according to the weighting.
+      Note, however, that this method does not yield the optimal rotation for non-uniform weighting,
+      as this would require an iterative, nonlinear optimization approach.
     reflection : bool
       If the transformation is allowed reflections
     translation : bool
@@ -241,56 +243,51 @@ def procrustes(
       The cost of the transformation
     """
 
-    a = np.asanyarray(a, dtype=np.float64)
-    b = np.asanyarray(b, dtype=np.float64)
-    if not util.is_shape(a, (-1, 3)) or not util.is_shape(b, (-1, 3)):
-        raise ValueError("points must be (n,3)!")
-    if len(a) != len(b):
-        raise ValueError("a and b must contain same number of points!")
-    if weights is not None:
-        w = np.asanyarray(weights, dtype=np.float64)
-        if len(w) != len(a):
-            raise ValueError("weights must have same length as a and b!")
-        w_norm = (w / w.sum()).reshape((-1, 1))
+    a_original = np.asanyarray(a, dtype=np.float64)
+    b_original = np.asanyarray(b, dtype=np.float64)
+    if not util.is_shape(a_original, (-1, 3)) or not util.is_shape(b_original, (-1, 3)):
+        raise ValueError('points must be (n,3)!')
+    if len(a_original) != len(b_original):
+        raise ValueError('a and b must contain same number of points!')
+    # weights are set to uniform if not provided.
+    if weights is None:
+        weights = np.ones(len(a_original))
+    w = np.maximum(np.asanyarray(weights, dtype=np.float64), 0)
+    if len(w) != len(a):
+        raise ValueError("weights must have same length as a and b!")
+    w_norm = (w / w.sum()).reshape((-1, 1))
+
+    # All zero entries are removed from further computations.
+    # If weights is a binary array, the optimal solution can still be found by simply removing the zero entries.
+    nonzero_weights = w_norm[:, 0] > 0
+    a_nonzero = a_original[nonzero_weights]
+    b_nonzero = b_original[nonzero_weights]
+    w_norm = w_norm[nonzero_weights]
 
     # Remove translation component
     if translation:
-        # acenter is a weighted average of the individual points.
-        if weights is None:
-            acenter = a.mean(axis=0)
-        else:
-            acenter = (a * w_norm).sum(axis=0)
-        bcenter = b.mean(axis=0)
+        # centers are (weighted) averages of the individual points.
+        acenter = (a_nonzero * w_norm).sum(axis=0)
+        bcenter = (b_nonzero * w_norm).sum(axis=0)
     else:
-        acenter = np.zeros(a.shape[1])
-        bcenter = np.zeros(b.shape[1])
+        acenter = np.zeros(a_nonzero.shape[1])
+        bcenter = np.zeros(b_nonzero.shape[1])
 
     # Remove scale component
     if scale:
-        if weights is None:
-            ascale = np.sqrt(((a - acenter) ** 2).sum() / len(a))
-            # ascale is the square root of weighted average of the
-            # squared difference
-            # between each point and acenter.
-        else:
-            ascale = np.sqrt((((a - acenter) ** 2) * w_norm).sum())
-
-        bscale = np.sqrt(((b - bcenter) ** 2).sum() / len(b))
+        # scale is the square root of the (weighted) average of the
+        # squared difference between each point and the center.
+        ascale = np.sqrt((((a_nonzero - acenter)**2) * w_norm).sum())
+        bscale = np.sqrt((((b_nonzero - bcenter)**2) * w_norm).sum())
     else:
         ascale = 1
         bscale = 1
 
     # Use SVD to find optimal orthogonal matrix R
     # constrained to det(R) = 1 if necessary.
-    # w_mat is multiplied with the centered and scaled a, such that the points
-    # can be weighted differently.
 
-    if weights is None:
-        target = np.dot(((b - bcenter) / bscale).T, ((a - acenter) / ascale))
-    else:
-        target = np.dot(
-            ((b - bcenter) / bscale).T, ((a - acenter) / ascale) * w.reshape((-1, 1))
-        )
+    target = np.dot(((b_nonzero - bcenter) / bscale).T,
+                    ((a_nonzero - acenter) / ascale))
 
     u, _s, vh = np.linalg.svd(target)
 
@@ -308,9 +305,11 @@ def procrustes(
     matrix = np.vstack((matrix, np.array([0.0] * (a.shape[1]) + [1.0]).reshape(1, -1)))
 
     if return_cost:
-        transformed = transform_points(a, matrix)
-        # return the mean euclidean distance squared as the cost
-        cost = ((b - transformed) ** 2).mean()
+        # Transform the original input array, including zero-weighted points
+        transformed = transform_points(a_original, matrix)
+        # The cost is the (weighted) sum of the euclidean distances between
+        # the transformed source points and the target points.
+        cost = (((b_nonzero - transformed[nonzero_weights])**2) * w_norm).sum()
         return matrix, transformed, cost
     else:
         return matrix