@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData(ExampleSet.class);
// only use numeric attributes
Tools.onlyNumericalAttributes(exampleSet, "KernelPCA");
Tools.onlyNonMissingValues(exampleSet, getOperatorClassName(), this);
Attributes attributes = exampleSet.getAttributes();
int numberOfExamples = exampleSet.size();
// calculating means for later zero centering
exampleSet.recalculateAllAttributeStatistics();
double[] means = new double[exampleSet.getAttributes().size()];
int i = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
means[i] = exampleSet.getStatistics(attribute, Statistics.AVERAGE);
i++;
}
// kernel
Kernel kernel = Kernel.createKernel(this);
// copying zero centered exampleValues
ArrayList<double[]> exampleValues = new ArrayList<double[]>(numberOfExamples);
i = 0;
for (Example columnExample : exampleSet) {
double[] columnValues = getAttributeValues(columnExample, attributes, means);
exampleValues.add(columnValues);
i++;
}
// filling kernel matrix
Matrix kernelMatrix = new Matrix(numberOfExamples, numberOfExamples);
for (i = 0; i < numberOfExamples; i++) {
for (int j = 0; j < numberOfExamples; j++) {
kernelMatrix.set(
i, j, kernel.calculateDistance(exampleValues.get(i), exampleValues.get(j)));
}
}
// calculating eigenVectors
EigenvalueDecomposition eig = kernelMatrix.eig();
Model model = new KernelPCAModel(exampleSet, means, eig.getV(), exampleValues, kernel);
if (exampleSetOutput.isConnected()) {
exampleSetOutput.deliver(model.apply(exampleSet));
}
originalOutput.deliver(exampleSet);
modelOutput.deliver(model);
}
@Override
public void init(ExampleSet exampleSet) throws OperatorException {
super.init(exampleSet);
Tools.onlyNumericalAttributes(exampleSet, "value based similarities");
Attributes attributes = exampleSet.getAttributes();
if (attributes.size() != 1)
throw new OperatorException(
"The bregman divergence you've choosen is not applicable for the dataset! Proceeding with the 'Squared Euclidean distance' bregman divergence.");
for (Example example : exampleSet) {
for (Attribute attribute : attributes) {
if (example.getValue(attribute) <= 0)
throw new OperatorException(
"The bregman divergence you've choosen is not applicable for the dataset! Proceeding with the 'Squared Euclidean distance' bregman divergence.");
;
}
}
}
@Override
public void init(ExampleSet exampleSet) throws OperatorException {
super.init(exampleSet);
Tools.onlyNumericalAttributes(exampleSet, "value based similarities");
}