private static int toColour(RealVector ambient) {
final double r = ambient.getEntry(0);
final double g = ambient.getEntry(1);
final double b = ambient.getEntry(2);
int rc = 256 * 256 * (int) (255. * r);
int rg = 256 * (int) (255. * g);
int rb = (int) (255. * b);
return rc + rg + rb;
}
@Override
public void train(List<Instance> instances) {
// ------------------------ initialize rows and columns ---------------------
int rows = instances.size();
int columns = 0;
// get max columns
for (Instance i : instances) {
int localColumns = Collections.max(i.getFeatureVector().getFeatureMap().keySet());
if (localColumns > columns) columns = localColumns;
}
// ------------------------ initialize alpha vector -----------------------
alpha = new ArrayRealVector(rows, 0);
// ------------------------ initialize base X and Y for use --------------------------
double[][] X = new double[rows][columns];
double[] Y = new double[rows];
for (int i = 0; i < rows; i++) {
Y[i] = ((ClassificationLabel) instances.get(i).getLabel()).getLabelValue();
for (int j = 0; j < columns; j++) {
X[i][j] = instances.get(i).getFeatureVector().get(j + 1);
}
}
// ---------------------- gram matrix -------------------
matrixX = new Array2DRowRealMatrix(X);
RealMatrix gram = new Array2DRowRealMatrix(rows, rows);
for (int i = 0; i < rows; i++) {
for (int j = 0; j < rows; j++) {
gram.setEntry(i, j, kernelFunction(matrixX.getRowVector(i), matrixX.getRowVector(j)));
}
}
// ---------------------- gradient ascent --------------------------
Sigmoid g = new Sigmoid(); // helper function
System.out.println("Training start...");
System.out.println(
"Learning rate: " + _learning_rate + " Training times: " + _training_iterations);
for (int idx = 0; idx < _training_iterations; idx++) {
System.out.println("Training iteration: " + (idx + 1));
for (int k = 0; k < rows; k++) {
double gradient_ascent = 0.0;
RealVector alpha_gram = gram.operate(alpha);
for (int i = 0; i < rows; i++) {
double lambda = alpha_gram.getEntry(i);
double kernel = gram.getEntry(i, k);
gradient_ascent =
gradient_ascent
+ Y[i] * g.value(-lambda) * kernel
+ (1 - Y[i]) * g.value(lambda) * (-kernel);
}
alpha.setEntry(k, alpha.getEntry(k) + _learning_rate * gradient_ascent);
}
}
System.out.println("Training done!");
}
@Override
public Label predict(Instance instance) {
Label l = null;
if (instance.getLabel() instanceof ClassificationLabel || instance.getLabel() == null) {
// ----------------- declare variables ------------------
double lambda = 0.0;
RealVector x_instance = new ArrayRealVector(matrixX.getColumnDimension(), 0);
double result = 0.0;
// -------------------------- initialize xi -------------------------
for (int idx = 0; idx < matrixX.getColumnDimension(); idx++) {
x_instance.setEntry(idx, instance.getFeatureVector().get(idx + 1));
}
// ------------------ get lambda -----------------------
for (int j = 0; j < alpha.getDimension(); j++) {
lambda += alpha.getEntry(j) * kernelFunction(matrixX.getRowVector(j), x_instance);
}
// ----------------- make prediction -----------------
Sigmoid g = new Sigmoid(); // helper function
result = g.value(lambda);
l = new ClassificationLabel(result < 0.5 ? 0 : 1);
} else {
System.out.println("label type error!");
}
return l;
}
private static Intersection getIntersection(
TriangleObject obj, DecompositionSolver solver, Vector3D p, Vector3D pc, double[] params) {
RealVector constants = new ArrayRealVector(params, false);
RealVector solution = solver.solve(constants);
double alpfa = solution.getEntry(0);
double beta = solution.getEntry(1);
boolean match = false;
if (alpfa >= 0 && beta >= 0 && alpfa + beta <= 1.0) {
match = true;
} else {
match = false;
}
final Intersection intersection = new Intersection(match);
intersection.setObject(obj);
intersection.setP(p);
return intersection;
}
public void update2DFixed() {
double[] delta = new double[Peak.NFITPARAMS];
double[] jt = new double[4];
double[] jacobian = new double[4];
double[][] hessian = new double[4][4];
for (FitPeak fit : this.fits) {
if (fit.peak.getStatus() == PeakStatus.RUNNING) {
for (int i = 0; i < 4; i++) {
jacobian[i] = 0.0;
hessian[i][0] = 0.0;
hessian[i][1] = 0.0;
hessian[i][2] = 0.0;
hessian[i][3] = 0.0;
}
int offset = fit.offset;
int wx = fit.wx;
int wy = fit.wy;
double height = fit.peak.getHeight();
double width = fit.peak.getXWidth();
for (int i = -wy; i <= +wy; i++) {
double yt = fit.yt[i + wy];
double eyt = fit.eyt[i + wy];
for (int j = -wx; j <= +wx; j++) {
int idx = (i * this.imgSizeX) + (j + offset);
// est = foreground + average background
double fi = this.fgData[idx] + (this.bgData[idx] / ((double) this.bgCounts[idx]));
double xi = this.imgData[idx];
double xt = fit.xt[j + wx];
double ext = fit.ext[j + wx];
double et = ext * eyt;
// TODO: Remember to change order to match peak array in peak class
jt[0] = et;
jt[1] = 2.0 * height * width * xt * et;
jt[2] = 2.0 * height * width * yt * et;
// TODO: this should be # 2
jt[3] = 1.0; // this is background
// calculate jacobian;
double t1 = 2.0 * (1.0 - xi / fi);
jacobian[0] += t1 * jt[0];
jacobian[1] += t1 * jt[1];
jacobian[2] += t1 * jt[2];
jacobian[3] += t1 * jt[3];
// calculate hessian (without second deriv terms)
double t2 = 2.0 * xi / (fi * fi);
hessian[0][0] += t2 * jt[0] * jt[0];
hessian[0][1] += t2 * jt[0] * jt[1];
hessian[0][2] += t2 * jt[0] * jt[2];
hessian[0][3] += t2 * jt[0] * jt[3];
// hessian[4]
hessian[1][1] += t2 * jt[1] * jt[1];
hessian[1][2] += t2 * jt[1] * jt[2];
hessian[1][3] += t2 * jt[1] * jt[3];
// hessian[8]
// hessian[9]
hessian[2][2] += t2 * jt[2] * jt[2];
hessian[2][3] += t2 * jt[2] * jt[3];
// hessian[12]
// hessian[13]
// hessian[14]
hessian[3][3] += t2 * jt[3] * jt[3];
}
}
// subtract old peak out of foreground and background arrays
subtractPeak(fit);
// use lapack to solve Ax=B to calculate update vector;
boolean error = false;
RealMatrix hessianMatrix = MatrixUtils.createRealMatrix(hessian);
RealVector jacobianVector = MatrixUtils.createRealVector(jacobian);
try {
MatrixUtils.solveUpperTriangularSystem(hessianMatrix, jacobianVector);
} catch (Exception ex) {
fit.peak.setStatus(PeakStatus.ERROR);
error = true;
}
if (!error) {
// update parameters
// height
// TODO: Rearranged the jacobian vector entries
delta[Peak.HEIGHT] = jacobianVector.getEntry(0); // height
delta[Peak.BACKGROUND] = jacobianVector.getEntry(3); // background
delta[Peak.XCENTER] = jacobianVector.getEntry(1); // x center
delta[Peak.YCENTER] = jacobianVector.getEntry(2); // y center
// update fits data
fitDataUpdate(fit, delta);
// add the new peak to the foreground and background arrays
if (!fit.peak.hasStatus(PeakStatus.ERROR)) {
addPeak(fit);
}
}
}
}
}
public void update2D() {
double[] delta = new double[Peak.NFITPARAMS];
double[] jt = new double[5];
double[] jacobian = new double[5];
double[][] hessian = new double[5][5];
for (FitPeak fit : this.fits) {
if (fit.peak.hasStatus(PeakStatus.RUNNING)) {
for (int i = 0; i < 5; i++) {
jacobian[i] = 0.0;
hessian[i][0] = 0.0;
hessian[i][1] = 0.0;
hessian[i][2] = 0.0;
hessian[i][3] = 0.0;
hessian[i][4] = 0.0;
}
final int offset = fit.offset;
final int wx = fit.wx;
final int wy = fit.wy;
final double height = fit.peak.getHeight();
final double width = fit.peak.getXWidth();
for (int i = -wy; i <= +wy; i++) {
final double yt = fit.yt[i + wy];
final double eyt = fit.eyt[i + wy];
for (int j = -wx; j <= +wx; j++) {
final double xt = fit.xt[j + wx];
final double ext = fit.ext[j + wx];
final int idx = (i * this.imgSizeX) + (j + offset);
final double xi = this.imgData[idx];
final double fi = this.fgData[idx] + (this.bgData[idx] / ((double) this.bgCounts[idx]));
final double et = ext * eyt;
jt[0] = et;
jt[1] = 2.0 * height * width * xt * et;
jt[2] = 2.0 * height * width * yt * et;
jt[3] = (-height * xt * xt * et) - (height * yt * yt * et);
jt[4] = 1.0;
// calculate jacobian
final double t1 = 2.0 * (1.0 - xi / fi);
jacobian[0] += t1 * jt[0];
jacobian[1] += t1 * jt[1];
jacobian[2] += t1 * jt[2];
jacobian[3] += t1 * jt[3];
jacobian[4] += t1 * jt[4];
// calculate hessian
final double t2 = 2.0 * xi / (fi * fi);
// calculate hessian without second derivative terms.
// (symmetric upper triangular)
hessian[0][0] += t2 * jt[0] * jt[0];
hessian[0][1] += t2 * jt[0] * jt[1];
hessian[0][2] += t2 * jt[0] * jt[2];
hessian[0][3] += t2 * jt[0] * jt[3];
hessian[0][4] += t2 * jt[0] * jt[4];
hessian[1][1] += t2 * jt[1] * jt[1];
hessian[1][2] += t2 * jt[1] * jt[2];
hessian[1][3] += t2 * jt[1] * jt[3];
hessian[1][4] += t2 * jt[1] * jt[4];
hessian[2][2] += t2 * jt[2] * jt[2];
hessian[2][3] += t2 * jt[2] * jt[3];
hessian[2][4] += t2 * jt[2] * jt[4];
hessian[3][3] += t2 * jt[3] * jt[3];
hessian[3][4] += t2 * jt[3] * jt[4];
hessian[4][4] += t2 * jt[4] * jt[4];
}
}
// subtract the old peak out of the foreground and background arrays
subtractPeak(fit);
// use lapack to solve Ax=B to calculate update vector;
boolean error = false;
final RealMatrix hessianMatrix = MatrixUtils.createRealMatrix(hessian);
RealVector jacobianVector = MatrixUtils.createRealVector(jacobian);
try {
MatrixUtils.solveUpperTriangularSystem(hessianMatrix, jacobianVector);
} catch (Exception ex) {
fit.peak.setStatus(PeakStatus.ERROR);
error = true;
}
if (!error) {
// TODO: Rearranged the jacobian vector entries
delta[Peak.HEIGHT] = jacobianVector.getEntry(0); // height
delta[Peak.XCENTER] = jacobianVector.getEntry(1); // x center
delta[Peak.YCENTER] = jacobianVector.getEntry(2); // y center
delta[Peak.XWIDTH] = jacobianVector.getEntry(3); // width
delta[Peak.YWIDTH] = jacobianVector.getEntry(3); // width
delta[Peak.BACKGROUND] = jacobianVector.getEntry(4); // background
// update fits data
fitDataUpdate(fit, delta);
// add the peak to the foreground and background arrays
// recalculate peak fit area as the peak width may have changed
if (!fit.peak.hasStatus(PeakStatus.ERROR)) {
fit.wx = calcWidth(fit.peak.getXWidth(), fit.wx);
fit.wy = fit.wx;
addPeak(fit);
}
}
}
}
}
public void updateZ() {
double[] delta = new double[Peak.NFITPARAMS];
double[] jt = new double[5];
double[] jacobian = new double[5];
double[][] hessian = new double[5][5];
for (FitPeak fit : this.fits) {
if (fit.peak.hasStatus(PeakStatus.RUNNING)) {
for (int i = 0; i < 5; i++) {
jacobian[i] = 0;
hessian[i][0] = 0.0;
hessian[i][1] = 0.0;
hessian[i][2] = 0.0;
hessian[i][3] = 0.0;
hessian[i][4] = 0.0;
}
final int offset = fit.offset;
final int wx = fit.wx;
final int wy = fit.wy;
final double height = fit.peak.getHeight();
final double xwidth = fit.peak.getXWidth();
final double ywidth = fit.peak.getYWidth();
// calculate dwx vs z
final double zCenter = fit.peak.getZCenter();
double z0 = (zCenter - this.wxZParams[1]) / this.wxZParams[2];
double z1 = z0 * z0;
double z2 = z1 * z0;
double zt = (2.0 * z0) + (3.0 * this.wxZParams[3] * z1) + (4.0 * this.wxZParams[4] * z2);
final double gx = -2.0 * zt / (this.wxZParams[0] * fit.wxTerm);
// calculate dwy vs z
z0 = (zCenter - this.wyZParams[1]) / this.wyZParams[2];
z1 = z0 * z0;
z2 = z1 * z0;
zt = (2.0 * z0) + (3.0 * this.wyZParams[3] * z1) + (4.0 * this.wyZParams[4] * z2);
final double gy = -2.0 * zt / (this.wyZParams[0] * fit.wyTerm);
for (int i = -wy; i < +wy; i++) {
final double yt = fit.yt[i + wy];
final double eyt = fit.eyt[i + wy];
for (int j = -wx; j < +wx; j++) {
final double xt = fit.xt[j + wx];
final double ext = fit.ext[j + wx];
final int idx = (i * this.imgSizeX) + (j + offset);
final double xi = this.imgData[idx];
final double fi = this.fgData[idx] / (this.bgData[idx] / ((double) this.bgCounts[idx]));
// first derivatives
final double et = ext * eyt;
jt[0] = et;
jt[1] = 2.0 * height * xwidth * xt * et;
jt[2] = 2.0 * height * ywidth * yt * et;
jt[3] = (-height * xt * xt * gx * et) - (height * yt * yt * gy * et);
jt[4] = 1.0;
// calculate jacobian
final double t1 = 2.0 * (1.0 - xi / fi);
jacobian[0] += t1 * jt[0];
jacobian[1] += t1 * jt[1];
jacobian[2] += t1 * jt[2];
jacobian[3] += t1 * jt[3];
jacobian[4] += t1 * jt[4];
// calculate hessian
final double t2 = 2.0 * xi / (fi * fi);
// calculate hessian without second derivative terms.
hessian[0][0] += t2 * jt[0] * jt[0];
hessian[0][1] += t2 * jt[0] * jt[1];
hessian[0][2] += t2 * jt[0] * jt[2];
hessian[0][3] += t2 * jt[0] * jt[3];
hessian[0][4] += t2 * jt[0] * jt[4];
hessian[1][1] += t2 * jt[1] * jt[1];
hessian[1][2] += t2 * jt[1] * jt[2];
hessian[1][3] += t2 * jt[1] * jt[3];
hessian[1][4] += t2 * jt[1] * jt[4];
hessian[2][2] += t2 * jt[2] * jt[2];
hessian[2][3] += t2 * jt[2] * jt[3];
hessian[2][4] += t2 * jt[2] * jt[4];
hessian[3][3] += t2 * jt[3] * jt[3];
hessian[3][4] += t2 * jt[3] * jt[4];
hessian[4][4] += t2 * jt[4] * jt[4];
}
}
// subtract the old peak out of the foreground and background arrays
subtractPeak(fit);
// use lapack to solve Ax=B to calculate update vector;
boolean error = false;
final RealMatrix hessianMatrix = MatrixUtils.createRealMatrix(hessian);
RealVector jacobianVector = MatrixUtils.createRealVector(jacobian);
try {
MatrixUtils.solveUpperTriangularSystem(hessianMatrix, jacobianVector);
} catch (Exception ex) {
System.out.println("Fitting ERROR:");
System.out.println(ex.getMessage());
fit.peak.setStatus(PeakStatus.ERROR);
error = true;
}
if (!error) {
// update parameters
delta[Peak.HEIGHT] = jacobianVector.getEntry(0);
delta[Peak.XCENTER] = jacobianVector.getEntry(1);
delta[Peak.YCENTER] = jacobianVector.getEntry(2);
delta[Peak.ZCENTER] = jacobianVector.getEntry(3);
delta[Peak.BACKGROUND] = jacobianVector.getEntry(4);
fitDataUpdate(fit, delta);
if (!fit.peak.hasStatus(PeakStatus.ERROR)) {
// calculate new x, y, width and update fit area
calcWidthsFromZ(fit);
fit.wx = calcWidth(fit.peak.getXWidth(), fit.wx);
fit.wy = calcWidth(fit.peak.getYWidth(), fit.wy);
addPeak(fit);
}
}
}
}
}
