private double[] getSubunitZDepth() {
int n = subunits.getSubunitCount();
double[] depth = new double[n];
Point3d probe = new Point3d();
// transform subunit centers into z-aligned position and calculate
// z-coordinates (depth) along the z-axis.
for (int i = 0; i < n; i++) {
Point3d p = subunits.getCenters().get(i);
probe.set(p);
transformationMatrix.transform(probe);
depth[i] = probe.z;
}
return depth;
}
