public void update() {
stressBeforeUpdate = stressAfterUpdate;
computeBofCoordinates();
BZ.multiply(newPositionMatrix, positionMatrix);
positionMatrix.set(newPositionMatrix);
vPlus.substituteBack(positionMatrix);
distances.set(new DistanceMatrix(positions));
stressAfterUpdate = stress();
iterations++;
}
public void initialize(
Space space, Matrix dissimilarities, List<Vector> positions, Matrix weights)
throws Exception {
this.space = space;
dimensions = positions.size();
positionSpace = new ListSpace(positions);
distances = new RowArrayMatrix(positionSpace, positionSpace);
distances.set(new DistanceMatrix(positions));
this.dissimilarities = new RowArrayMatrix(dissimilarities);
this.positions = positions;
if (weights != null) this.weights = new RowArrayMatrix(weights);
else {
this.weights = new RowArrayMatrix(positionSpace, positionSpace);
this.weights.ones();
}
newPositions = new ArrayList<Vector>();
for (int i = 0; i < positions.size(); i++) newPositions.add(new ArrayVector(space));
positionMatrix = new RowVectorMatrix(positions, space);
newPositionMatrix = new RowVectorMatrix(newPositions, space);
normalizeWeights();
vPlus = computeVPlus(this.weights);
stressBeforeUpdate = Double.MAX_VALUE;
stressAfterUpdate = stress();
iterations = 0;
BZ = new RowArrayMatrix(positionSpace, positionSpace);
}
public void dump() {
System.out.println("Distances:");
distances.dump();
System.out.println("Coordinates:");
for (Vector coordinate : positions) coordinate.dump();
System.out.println("Stress: " + stressAfterUpdate);
}
private PermutedLUDecomposition computeVPlus(RowArrayMatrix weights) throws Exception {
RowArrayMatrix V = new RowArrayMatrix(positionSpace, positionSpace);
for (int i = 0; i < dimensions; i++) {
for (int j = 0; j < dimensions; j++) {
if (i == j) {
double sum = 0;
for (int k = 0; k < dimensions; k++) if (k != i) sum += weights.values[i][k];
V.values[i][j] = sum;
} else V.values[i][j] = -weights.values[i][j];
}
}
V.add(1);
return new PermutedLUDecomposition(V);
}
private void normalizeWeights() {
weights.setMainDiagonal(0);
weights.divide(weights.maximum());
weights.setMainDiagonal(1);
}
