analyzes the distribution of a set of shapes using Procrustes analysis.
This analysis method matches landmark data (geometric locations representing
significant features in a given shape) to calculate the best shape-preserving
Euclidian transformations. These transformations minimize the differences
in location between compared landmark data.
Procrustes analysis is also useful in conjunction with multidimensional
scaling. In Example: Multidimensional Scaling there is an observation
that the orientation of the reconstructed points is arbitrary. Two
different applications of multidimensional scaling could produce reconstructed
points that are very similar in principle, but that look different
because they have different orientations. The
transforms one set of points to make them more comparable to the other.
takes two matrices as input:
The target shape matrix X has dimension
n is the number of landmarks in the shape
p is the number of measurements per landmark.
The comparison shape matrix Y has
If there are fewer measurements per landmark for the comparison shape
than the target shape (
the function adds columns of zeros to Y, yielding
The equation to obtain the transformed shape, Z, is
b is a scaling factor that stretches (b > 1) or shrinks (b < 1) the points.
T is the orthogonal rotation and reflection matrix.
c is a matrix with constant values in each column, used to shift the points.
procrustes function chooses b, T,
and c to minimize the distance between the target
shape X and the transformed shape Z as
measured by the least squares criterion:
Procrustes analysis is appropriate when all
dimensions have similar scales. The analysis would be inaccurate,
for example, if the columns of Z had different
The first column is measured in milliliters ranging from 2,000 to 6,000.
The second column is measured in degrees Celsius ranging from 10 to 25.
The third column is measured in kilograms ranging from 50 to 230.
In such cases, standardize your variables by:
Subtracting the sample mean from each variable.
Dividing each resultant variable by its sample standard deviation.
to perform this standardization.
In this example, use Procrustes analysis to compare two handwritten number threes. Visually and analytically explore the effects of forcing size and reflection changes as follows:
Input landmark data for two handwritten number threes:
A = [11 39;17 42;25 42;25 40;23 36;19 35;30 34;35 29;... 30 20;18 19]; B = [15 31;20 37;30 40;29 35;25 29;29 31;31 31;35 20;... 29 10;25 18];
B to the side to make each shape more visible:
X = A; Y = B + repmat([25 0], 10,1);
plot(X(:,1), X(:,2),'r-', Y(:,1), Y(:,2),'b-'); text(X(:,1), X(:,2),('abcdefghij')') text(Y(:,1), Y(:,2),('abcdefghij')') legend('X = Target','Y = Comparison','location','SE') set(gca,'YLim',[0 55],'XLim',[0 65]);
Use Procrustes analysis to find the transformation that minimizes distances between landmark data points.
procrustes as follows:
[d, Z, tr] = procrustes(X,Y);
d – A standardized dissimilarity
Z – A matrix of the transformed
tr – A structure array of
the computed transformation with fields
c which correspond to the transformation equation, Equation 13-1.
Visualize the transformed shape,
a dashed blue line:
plot(X(:,1), X(:,2),'r-', Y(:,1), Y(:,2),'b-',... Z(:,1),Z(:,2),'b:'); text(X(:,1), X(:,2),('abcdefghij')') text(Y(:,1), Y(:,2),('abcdefghij')') text(Z(:,1), Z(:,2),('abcdefghij')') legend('X = Target','Y = Comparison',... 'Z = Transformed','location','SW') set(gca,'YLim',[0 55],'XLim',[0 65]);
Use two different numerical values to assess the similarity of the target shape and the transformed shape.
Dissimilarity Measure d. The dissimilarity measure
d gives a number
between 0 and 1 describing the difference between the target shape
and the transformed shape. Values near 0 imply more similar shapes,
while values near 1 imply dissimilarity. For this example:
d = 0.1502
din this case shows that the two shapes are similar.
comparing the sum of squared deviations between the set of points
with the sum of squared deviations of the original points from their
numerator = sum(sum((X-Z).^2)) numerator = 166.5321 denominator = sum(sum(bsxfun(@minus,X,mean(X)).^2)) denominator = 1.1085e+003 ratio = numerator/denominator ratio = 0.1502
The resulting measure
Examine the Scaling Measure b. The target and comparison threes in the previous figure visually
show that the two numbers are of a similar size. The closeness of
calculated value of the scaling factor
b to 1 supports
this observation as well:
tr.b ans = 0.9291
The sizes of the target and comparison shapes appear similar.
This visual impression is reinforced by the value of
0.93, which implies that the best transformation results in shrinking
the comparison shape by a factor .93 (only 7%).
Explore the effects of manually adjusting the scaling and reflection coefficients.
Fix the Scaling Factor
b = 1. Force
b to equal 1 (set
to examine the amount of dissimilarity in size of the target and transformed
ds = procrustes(X,Y,'Scaling',false) ds = 0.1552
In this case, setting
the calculated value of
d only 0.0049, which further
supports the similarity in the size of the two number threes. A larger
d would have indicated a greater size
Force a Reflection in the Transformation. This example requires only a rotation, not a reflection, to
align the shapes. You can show this by observing that the determinant
of the matrix
T is 1 in this analysis:
det(tr.T) ans = 1.0000
If you need a reflection in the transformation, the determinant
T is -1. You can force a reflection into the
transformation as follows:
[dr,Zr,trr] = procrustes(X,Y,'Reflection',true); dr dr = 0.8130
d value increases dramatically, indicating
that a forced reflection leads to a poor transformation of the landmark
points. A plot of the transformed shape shows a similar result:
The landmark data points are now further away from their target counterparts.
The transformed three is now an undesirable mirror image of the target three.
plot(X(:,1), X(:,2),'r-', Y(:,1), Y(:,2),'b-',... Zr(:,1),Zr(:,2),'b:'); text(X(:,1), X(:,2),('abcdefghij')') text(Y(:,1), Y(:,2),('abcdefghij')') text(Zr(:,1), Zr(:,2),('abcdefghij')') legend('X = Target','Y = Comparison',... 'Z = Transformed','location','SW') set(gca,'YLim',[0 55],'XLim',[0 65]);
It appears that the shapes might be better matched if you flipped the transformed shape upside down. Flipping the shapes would make the transformation even worse, however, because the landmark data points would be further away from their target counterparts. From this example, it is clear that manually adjusting the scaling and reflection parameters is generally not optimal.