public int rank(double effectiveZero) {
DenseMatrix svdDude;
if (this instanceof DenseMatrix) {
svdDude = (DenseMatrix) this;
} else {
svdDude = new DenseMatrix(this);
}
SingularValueDecomposition svd = SingularValueDecompositionMTJ.create(svdDude);
return svd.effectiveRank(effectiveZero);
}
/**
* Test of learn method, of class gov.sandia.cognition.learning.pca.PrincipalComponentsAnalysis.
*
* <p>The example data is based on: http://www.kernel-machines.org/code/kpca_toy.m
*/
public void testPCALearn() {
System.out.println("PCA.learn");
int num = random.nextInt(100) + 10;
ArrayList<Vector> data = new ArrayList<Vector>(num);
final double r1 = random.nextDouble();
final double r2 = r1 / random.nextDouble();
for (int i = 0; i < num; i++) {
data.add(VectorFactory.getDefault().createUniformRandom(INPUT_DIM, r1, r2, random));
}
Vector mean = MultivariateStatisticsUtil.computeMean(data);
DenseMatrix X = DenseMatrixFactoryMTJ.INSTANCE.createMatrix(INPUT_DIM, num);
for (int n = 0; n < num; n++) {
X.setColumn(n, data.get(n).minus(mean));
}
final ArrayList<Vector> dataCopy = ObjectUtil.cloneSmartElementsAsArrayList(data);
long startsvd = System.currentTimeMillis();
SingularValueDecomposition svd = SingularValueDecompositionMTJ.create(X);
long stopsvd = System.currentTimeMillis();
long start = System.currentTimeMillis();
PrincipalComponentsAnalysis instance = this.createPCAInstance();
PrincipalComponentsAnalysisFunction f = instance.learn(data);
long stop = System.currentTimeMillis();
assertEquals(dataCopy, data);
System.out.println("Uhat:\n" + f.getDimensionReducer().getDiscriminant().transpose());
System.out.println("U:\n" + svd.getU());
System.out.println("Time taken: SVD = " + (stopsvd - startsvd) + ", PCA = " + (stop - start));
// Make sure the PCA algorithm subtracted off the sample mean
if (mean.equals(f.getMean(), 1e-5) == false) {
assertEquals(mean, f.getMean());
}
assertEquals(OUTPUT_DIM, instance.getNumComponents());
assertEquals(instance.getNumComponents(), f.getOutputDimensionality());
assertEquals(INPUT_DIM, f.getInputDimensionality());
if (mean.equals(f.getMean(), 1e-5) == false) {
assertEquals(mean, f.getMean());
}
double absnorm = 0.0;
int nc = instance.getNumComponents() * INPUT_DIM;
for (int i = 0; i < instance.getNumComponents(); i++) {
Vector uihat = f.getDimensionReducer().getDiscriminant().getRow(i);
for (int j = 0; j < i; j++) {
Vector ujhat = f.getDimensionReducer().getDiscriminant().getRow(j);
assertEquals(
"Dot product between " + i + " and " + j + " is too large!",
0.0,
uihat.dotProduct(ujhat),
1e-2);
}
assertEquals(1.0, uihat.norm2(), 1e-5);
Vector ui = svd.getU().getColumn(i);
absnorm += Math.min(ui.minus(uihat).norm2(), ui.minus(uihat.scale(-1)).norm2());
}
absnorm /= nc;
System.out.println("U 1-norm: " + absnorm);
assertEquals(0.0, absnorm, 1e-1);
}