private Matrix walk() throws IOException {
// Step 0. Initialise transition probabilities
this.logger.showTimedMessage("Initialise transition probabilities");
Matrix P = this.initialiseTransitionProbabilities();
logger.showMemoryUsage();
// 2. initialise random walkers.
// keep in mind that this makes sense because of the way the indexes were
// loaded into this.goTermIndex. Otherwise, we would have to retrieve
// from this.goTermIndex
Matrix W = new Matrix(this.getNumGoTerms(), this.getNumGoTerms());
for (int i = 0; i < this.getNumGoTerms(); i++) {
W.set(i, i, 1.0f);
}
// walk!
Matrix W_star = W.copy();
double convergence;
// int i=0;
do {
W = W_star;
W_star = P.times(W);
convergence = W_star.minus(W).normF();
this.logger.showTimedMessage(
"\t Convergence difference: " + (new Double(convergence)).toString());
// this.logger.showTimedMessage("\t Doing iteration i=" + i);
// i++;
// }while (i<15);
} while (convergence > this.epsilon);
return W_star;
}
/**
* Returns C = A + b, where b is a scalar
*
* @param val
* @return
*/
public MatrixObject scalarAdd(int val) {
Matrix m = matrix.copy();
for (int i = 0; i < rows(); i++) {
for (int j = 0; j < cols(); j++) {
m.set(i, j, m.get(i, j) + val);
}
}
return new MatrixObject(m);
}
/**
* Creation of one muscle.
*
* @param moment nb_segment lines, 3 col : On each line, the influence on the given joint as in
* moment[i,0]+moment[i,1]*sin(moment[i,2]*angle)
* @param minL0 minimum size of muscle
* @param maxL0 maximum size of muscle
*/
public SimpleMuscle() {
// Init
_ln = _minL0.copy();
_vn = new Matrix(1, _ln.getColumnDimension(), 0);
_tn = new Matrix(1, _ln.getColumnDimension(), 0);
_t = new Matrix(1, _ln.getColumnDimension(), 0);
_cpl = new Matrix(1, _minA.getColumnDimension(), 0);
// ratio l/l0=k
// _k = (_maxL0-_minL0) / JamaU.dotP(_mom, _maxA.minus(_minA));
_k = (_maxL0.minus(_minL0)).arrayRightDivide((_maxA.minus(_minA)).times(_mom.transpose()));
_k = _k.uminus();
}
@Override
public CalcObject plus() {
return new MatrixObject(matrix.copy());
}
private void RunSPKF() {
// SPKF Steps:
// 1) Generate Test Points
// 2) Propagate Test Points
// 3) Compute Predicted Mean and Covariance
// 4) Compute Measurements
// 5) Compute Innovations and Cross Covariance
// 6) Compute corrections and update
// Line up initial variables from the controller!
Double dAlpha = dGreek.get(0);
Double dBeta = dGreek.get(1);
cController.setAlpha(dAlpha);
cController.setBeta(dBeta);
cController.setKappa(dGreek.get(2));
Double dGamma = cController.getGamma();
Double dLambda = cController.getLambda();
// // DEBUG - Print the Greeks
// System.out.println("Greeks!");
// System.out.println("Alpha - " + dAlpha);
// System.out.println("Beta - " + dBeta);
// System.out.println("Kappa - " + dGreek.get(2));
// System.out.println("Lambda - " + dLambda);
// System.out.println("Gamma - " + dGamma);
// Let's get started:
// Step 1: Generate Test Points
Vector<Matrix> Chi = new Vector<Matrix>();
Vector<Matrix> UpChi = new Vector<Matrix>();
Vector<Matrix> UpY = new Vector<Matrix>();
Matrix UpPx = new Matrix(3, 3, 0.0);
Matrix UpPy = new Matrix(3, 3, 0.0);
Matrix UpPxy = new Matrix(3, 3, 0.0);
Matrix K;
Vector<Double> wc = new Vector<Double>();
Vector<Double> wm = new Vector<Double>();
Chi.add(X); // Add Chi_0 - the current state estimate (X, Y, Z)
// Big P Matrix is LxL diagonal
Matrix SqrtP = SqrtSPKF(P);
SqrtP = SqrtP.times(dGamma);
// Set up Sigma Points
for (int i = 0; i <= 8; i++) {
Matrix tempVec = SqrtP.getMatrix(0, 8, i, i);
Matrix tempX = X;
Matrix tempPlus = tempX.plus(tempVec);
// System.out.println("TempPlus");
// tempPlus.print(3, 2);
Matrix tempMinu = tempX.minus(tempVec);
// System.out.println("TempMinus");
// tempMinu.print(3, 2);
// tempX = X.copy();
// tempX.setMatrix(i, i, 0, 2, tempPlus);
Chi.add(tempPlus);
// tempX = X.copy();
// tempX.setMatrix(i, i, 0, 2, tempMinu);
Chi.add(tempMinu);
}
// DEBUG Print the lines inside the Chi Matrix (2L x L)
// for (int i = 0; i<=(2*L); i++){
// System.out.println("Chi Matrix Set: "+i);
// Chi.get(i).print(5, 2);
// }
// Generate weights
Double WeightZero = (dLambda / (L + dLambda));
Double OtherWeight = (1 / (2 * (L + dLambda)));
Double TotalWeight = WeightZero;
wm.add(WeightZero);
wc.add(WeightZero + (1 - (dAlpha * dAlpha) + dBeta));
for (int i = 1; i <= (2 * L); i++) {
TotalWeight = TotalWeight + OtherWeight;
wm.add(OtherWeight);
wc.add(OtherWeight);
}
// Weights MUST BE 1 in total
for (int i = 0; i <= (2 * L); i++) {
wm.set(i, wm.get(i) / TotalWeight);
wc.set(i, wc.get(i) / TotalWeight);
}
// //DEBUG Print the weights
// System.out.println("Total Weight:");
// System.out.println(TotalWeight);
// for (int i = 0; i<=(2*L); i++){
// System.out.println("Weight M for "+i+" Entry");
// System.out.println(wm.get(i));
// System.out.println("Weight C for "+i+" Entry");
// System.out.println(wc.get(i));
// }
// Step 2: Propagate Test Points
// This will also handle computing the mean
Double ux = dControl.elementAt(0);
Double uy = dControl.elementAt(1);
Double uz = dControl.elementAt(2);
Matrix XhatMean = new Matrix(3, 1, 0.0);
for (int i = 0; i < Chi.size(); i++) {
Matrix ChiOne = Chi.get(i);
Matrix Chixminus = new Matrix(3, 1, 0.0);
Double Xhat = ChiOne.get(0, 0);
Double Yhat = ChiOne.get(1, 0);
Double Zhat = ChiOne.get(2, 0);
Double Xerr = ChiOne.get(3, 0);
Double Yerr = ChiOne.get(4, 0);
Double Zerr = ChiOne.get(5, 0);
Xhat = Xhat + ux + Xerr;
Yhat = Yhat + uy + Yerr;
Zhat = Zhat + uz + Zerr;
Chixminus.set(0, 0, Xhat);
Chixminus.set(1, 0, Yhat);
Chixminus.set(2, 0, Zhat);
// System.out.println("ChixMinus:");
// Chixminus.print(3, 2);
UpChi.add(Chixminus);
XhatMean = XhatMean.plus(Chixminus.times(wm.get(i)));
}
// Mean is right!
// System.out.println("XhatMean: ");
// XhatMean.print(3, 2);
// Step 3: Compute Predicted Mean and Covariance
// Welp, we already solved the mean - let's do the covariance now
for (int i = 0; i <= (2 * L); i++) {
Matrix tempP = UpChi.get(i).minus(XhatMean);
Matrix tempPw = tempP.times(wc.get(i));
tempP = tempPw.times(tempP.transpose());
UpPx = UpPx.plus(tempP);
}
// New Steps!
// Step 4: Compute Measurements! (and Y mean!)
Matrix YhatMean = new Matrix(3, 1, 0.0);
for (int i = 0; i <= (2 * L); i++) {
Matrix ChiOne = Chi.get(i);
Matrix Chiyminus = new Matrix(3, 1, 0.0);
Double Xhat = UpChi.get(i).get(0, 0);
Double Yhat = UpChi.get(i).get(1, 0);
Double Zhat = UpChi.get(i).get(2, 0);
Double Xerr = ChiOne.get(6, 0);
Double Yerr = ChiOne.get(7, 0);
Double Zerr = ChiOne.get(8, 0);
Xhat = Xhat + Xerr;
Yhat = Yhat + Yerr;
Zhat = Zhat + Zerr;
Chiyminus.set(0, 0, Xhat);
Chiyminus.set(1, 0, Yhat);
Chiyminus.set(2, 0, Zhat);
UpY.add(Chiyminus);
YhatMean = YhatMean.plus(Chiyminus.times(wm.get(i)));
}
// // Welp, we already solved the mean - let's do the covariances
// now
// System.out.println("XHatMean and YHatMean = ");
// XhatMean.print(3, 2);
// YhatMean.print(3, 2);
for (int i = 0; i <= (2 * L); i++) {
Matrix tempPx = UpChi.get(i).minus(XhatMean);
Matrix tempPy = UpY.get(i).minus(YhatMean);
// System.out.println("ChiX - XhatMean and ChiY-YhatMean");
// tempPx.print(3, 2);
// tempPy.print(3, 2);
Matrix tempPxw = tempPx.times(wc.get(i));
Matrix tempPyw = tempPy.times(wc.get(i));
tempPx = tempPxw.times(tempPy.transpose());
tempPy = tempPyw.times(tempPy.transpose());
UpPy = UpPy.plus(tempPy);
UpPxy = UpPxy.plus(tempPx);
}
// Step 6: Compute Corrections and Update
// Compute Kalman Gain!
// System.out.println("Updated Px");
// UpPx.print(5, 2);
// System.out.println("Updated Py");
// UpPy.print(5, 2);
// System.out.println("Updated Pxy");
// UpPxy.print(5, 2);
K = UpPxy.times(UpPy.inverse());
// System.out.println("Kalman");
// K.print(5, 2);
Matrix Mea = new Matrix(3, 1, 0.0);
Mea.set(0, 0, dMeasure.get(0));
Mea.set(1, 0, dMeasure.get(1));
Mea.set(2, 0, dMeasure.get(2));
Matrix Out = K.times(Mea.minus(YhatMean));
Out = Out.plus(XhatMean);
// System.out.println("Out:");
// Out.print(3, 2);
Matrix Px = UpPx.minus(K.times(UpPy.times(K.transpose())));
// Update Stuff!
// Push the P to the controller
Matrix OutP = P.copy();
OutP.setMatrix(0, 2, 0, 2, Px);
X.setMatrix(0, 2, 0, 0, Out);
Residual = XhatMean.minus(Out);
cController.inputState(OutP, Residual);
// cController.setL(L);
cController.startProcess();
while (!cController.finishedProcess()) {
try {
Thread.sleep(10);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
// System.out.println("Post Greeks: " + cController.getAlpha() + " ,
// "+ cController.getBeta());
dGreek.set(0, cController.getAlpha());
dGreek.set(1, cController.getBeta());
dGreek.set(2, cController.getKappa());
P = cController.getP();
// System.out.println("P is post Process:");
// P.print(3, 2);
StepDone = true;
}
public static void main(String argv[]) {
Matrix A, B, C, Z, O, I, R, S, X, SUB, M, T, SQ, DEF, SOL;
// Uncomment this to test IO in a different locale.
// Locale.setDefault(Locale.GERMAN);
int errorCount = 0;
int warningCount = 0;
double tmp, s;
double[] columnwise = {1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12.};
double[] rowwise = {1., 4., 7., 10., 2., 5., 8., 11., 3., 6., 9., 12.};
double[][] avals = {{1., 4., 7., 10.}, {2., 5., 8., 11.}, {3., 6., 9., 12.}};
double[][] rankdef = avals;
double[][] tvals = {{1., 2., 3.}, {4., 5., 6.}, {7., 8., 9.}, {10., 11., 12.}};
double[][] subavals = {{5., 8., 11.}, {6., 9., 12.}};
double[][] rvals = {{1., 4., 7.}, {2., 5., 8., 11.}, {3., 6., 9., 12.}};
double[][] pvals = {{4., 1., 1.}, {1., 2., 3.}, {1., 3., 6.}};
double[][] ivals = {{1., 0., 0., 0.}, {0., 1., 0., 0.}, {0., 0., 1., 0.}};
double[][] evals = {
{0., 1., 0., 0.}, {1., 0., 2.e-7, 0.}, {0., -2.e-7, 0., 1.}, {0., 0., 1., 0.}
};
double[][] square = {{166., 188., 210.}, {188., 214., 240.}, {210., 240., 270.}};
double[][] sqSolution = {{13.}, {15.}};
double[][] condmat = {{1., 3.}, {7., 9.}};
double[][] badeigs = {
{0, 0, 0, 0, 0}, {0, 0, 0, 0, 1}, {0, 0, 0, 1, 0}, {1, 1, 0, 0, 1}, {1, 0, 1, 0, 1}
};
int rows = 3, cols = 4;
int invalidld = 5; /* should trigger bad shape for construction with val */
int raggedr = 0; /* (raggedr,raggedc) should be out of bounds in ragged array */
int raggedc = 4;
int validld = 3; /* leading dimension of intended test Matrices */
int nonconformld = 4; /* leading dimension which is valid, but nonconforming */
int ib = 1, ie = 2, jb = 1, je = 3; /* index ranges for sub Matrix */
int[] rowindexset = {1, 2};
int[] badrowindexset = {1, 3};
int[] columnindexset = {1, 2, 3};
int[] badcolumnindexset = {1, 2, 4};
double columnsummax = 33.;
double rowsummax = 30.;
double sumofdiagonals = 15;
double sumofsquares = 650;
/**
* Constructors and constructor-like methods: double[], int double[][] int, int int, int, double
* int, int, double[][] constructWithCopy(double[][]) random(int,int) identity(int)
*/
print("\nTesting constructors and constructor-like methods...\n");
try {
/** check that exception is thrown in packed constructor with invalid length * */
A = new Matrix(columnwise, invalidld);
errorCount =
try_failure(
errorCount,
"Catch invalid length in packed constructor... ",
"exception not thrown for invalid input");
} catch (IllegalArgumentException e) {
try_success("Catch invalid length in packed constructor... ", e.getMessage());
}
try {
/** check that exception is thrown in default constructor if input array is 'ragged' * */
A = new Matrix(rvals);
tmp = A.get(raggedr, raggedc);
} catch (IllegalArgumentException e) {
try_success("Catch ragged input to default constructor... ", e.getMessage());
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"Catch ragged input to constructor... ",
"exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later");
}
try {
/** check that exception is thrown in constructWithCopy if input array is 'ragged' * */
A = Matrix.constructWithCopy(rvals);
tmp = A.get(raggedr, raggedc);
} catch (IllegalArgumentException e) {
try_success("Catch ragged input to constructWithCopy... ", e.getMessage());
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"Catch ragged input to constructWithCopy... ",
"exception not thrown in construction...ArrayIndexOutOfBoundsException thrown later");
}
A = new Matrix(columnwise, validld);
B = new Matrix(avals);
tmp = B.get(0, 0);
avals[0][0] = 0.0;
C = B.minus(A);
avals[0][0] = tmp;
B = Matrix.constructWithCopy(avals);
tmp = B.get(0, 0);
avals[0][0] = 0.0;
if ((tmp - B.get(0, 0)) != 0.0) {
/** check that constructWithCopy behaves properly * */
errorCount =
try_failure(
errorCount, "constructWithCopy... ", "copy not effected... data visible outside");
} else {
try_success("constructWithCopy... ", "");
}
avals[0][0] = columnwise[0];
I = new Matrix(ivals);
try {
check(I, Matrix.identity(3, 4));
try_success("identity... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "identity... ", "identity Matrix not successfully created");
}
/**
* Access Methods: getColumnDimension() getRowDimension() getArray() getArrayCopy()
* getColumnPackedCopy() getRowPackedCopy() get(int,int) getMatrix(int,int,int,int)
* getMatrix(int,int,int[]) getMatrix(int[],int,int) getMatrix(int[],int[]) set(int,int,double)
* setMatrix(int,int,int,int,Matrix) setMatrix(int,int,int[],Matrix)
* setMatrix(int[],int,int,Matrix) setMatrix(int[],int[],Matrix)
*/
print("\nTesting access methods...\n");
/** Various get methods: */
B = new Matrix(avals);
if (B.getRowDimension() != rows) {
errorCount = try_failure(errorCount, "getRowDimension... ", "");
} else {
try_success("getRowDimension... ", "");
}
if (B.getColumnDimension() != cols) {
errorCount = try_failure(errorCount, "getColumnDimension... ", "");
} else {
try_success("getColumnDimension... ", "");
}
B = new Matrix(avals);
double[][] barray = B.getArray();
if (barray != avals) {
errorCount = try_failure(errorCount, "getArray... ", "");
} else {
try_success("getArray... ", "");
}
barray = B.getArrayCopy();
if (barray == avals) {
errorCount = try_failure(errorCount, "getArrayCopy... ", "data not (deep) copied");
}
try {
check(barray, avals);
try_success("getArrayCopy... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "getArrayCopy... ", "data not successfully (deep) copied");
}
double[] bpacked = B.getColumnPackedCopy();
try {
check(bpacked, columnwise);
try_success("getColumnPackedCopy... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"getColumnPackedCopy... ",
"data not successfully (deep) copied by columns");
}
bpacked = B.getRowPackedCopy();
try {
check(bpacked, rowwise);
try_success("getRowPackedCopy... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "getRowPackedCopy... ", "data not successfully (deep) copied by rows");
}
try {
tmp = B.get(B.getRowDimension(), B.getColumnDimension() - 1);
errorCount =
try_failure(
errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
tmp = B.get(B.getRowDimension() - 1, B.getColumnDimension());
errorCount =
try_failure(
errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("get(int,int)... OutofBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount, "get(int,int)... ", "OutOfBoundsException expected but not thrown");
}
try {
if (B.get(B.getRowDimension() - 1, B.getColumnDimension() - 1)
!= avals[B.getRowDimension() - 1][B.getColumnDimension() - 1]) {
errorCount =
try_failure(
errorCount, "get(int,int)... ", "Matrix entry (i,j) not successfully retreived");
} else {
try_success("get(int,int)... ", "");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(errorCount, "get(int,int)... ", "Unexpected ArrayIndexOutOfBoundsException");
}
SUB = new Matrix(subavals);
try {
M = B.getMatrix(ib, ie + B.getRowDimension() + 1, jb, je);
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
M = B.getMatrix(ib, ie, jb, je + B.getColumnDimension() + 1);
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("getMatrix(int,int,int,int)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
M = B.getMatrix(ib, ie, jb, je);
try {
check(SUB, M);
try_success("getMatrix(int,int,int,int)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int,int)... ",
"submatrix not successfully retreived");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int,int)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
M = B.getMatrix(ib, ie, badcolumnindexset);
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
M = B.getMatrix(ib, ie + B.getRowDimension() + 1, columnindexset);
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("getMatrix(int,int,int[])... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
M = B.getMatrix(ib, ie, columnindexset);
try {
check(SUB, M);
try_success("getMatrix(int,int,int[])... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "getMatrix(int,int,int[])... ", "submatrix not successfully retreived");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"getMatrix(int,int,int[])... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
M = B.getMatrix(badrowindexset, jb, je);
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
M = B.getMatrix(rowindexset, jb, je + B.getColumnDimension() + 1);
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("getMatrix(int[],int,int)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int,int)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
M = B.getMatrix(rowindexset, jb, je);
try {
check(SUB, M);
try_success("getMatrix(int[],int,int)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "getMatrix(int[],int,int)... ", "submatrix not successfully retreived");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int,int)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
M = B.getMatrix(badrowindexset, columnindexset);
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
M = B.getMatrix(rowindexset, badcolumnindexset);
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("getMatrix(int[],int[])... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int[])... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
M = B.getMatrix(rowindexset, columnindexset);
try {
check(SUB, M);
try_success("getMatrix(int[],int[])... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "getMatrix(int[],int[])... ", "submatrix not successfully retreived");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
errorCount =
try_failure(
errorCount,
"getMatrix(int[],int[])... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
/** Various set methods: */
try {
B.set(B.getRowDimension(), B.getColumnDimension() - 1, 0.);
errorCount =
try_failure(
errorCount,
"set(int,int,double)... ",
"OutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
B.set(B.getRowDimension() - 1, B.getColumnDimension(), 0.);
errorCount =
try_failure(
errorCount,
"set(int,int,double)... ",
"OutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("set(int,int,double)... OutofBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"set(int,int,double)... ",
"OutOfBoundsException expected but not thrown");
}
try {
B.set(ib, jb, 0.);
tmp = B.get(ib, jb);
try {
check(tmp, 0.);
try_success("set(int,int,double)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "set(int,int,double)... ", "Matrix element not successfully set");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
errorCount =
try_failure(
errorCount, "set(int,int,double)... ", "Unexpected ArrayIndexOutOfBoundsException");
}
M = new Matrix(2, 3, 0.);
try {
B.setMatrix(ib, ie + B.getRowDimension() + 1, jb, je, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
B.setMatrix(ib, ie, jb, je + B.getColumnDimension() + 1, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("setMatrix(int,int,int,int,Matrix)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
B.setMatrix(ib, ie, jb, je, M);
try {
check(M.minus(B.getMatrix(ib, ie, jb, je)), M);
try_success("setMatrix(int,int,int,int,Matrix)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int,int,Matrix)... ",
"submatrix not successfully set");
}
B.setMatrix(ib, ie, jb, je, SUB);
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int,int,Matrix)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
B.setMatrix(ib, ie + B.getRowDimension() + 1, columnindexset, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
B.setMatrix(ib, ie, badcolumnindexset, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("setMatrix(int,int,int[],Matrix)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
B.setMatrix(ib, ie, columnindexset, M);
try {
check(M.minus(B.getMatrix(ib, ie, columnindexset)), M);
try_success("setMatrix(int,int,int[],Matrix)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int[],Matrix)... ",
"submatrix not successfully set");
}
B.setMatrix(ib, ie, jb, je, SUB);
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int,int,int[],Matrix)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
B.setMatrix(rowindexset, jb, je + B.getColumnDimension() + 1, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
B.setMatrix(badrowindexset, jb, je, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("setMatrix(int[],int,int,Matrix)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int,int,Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
B.setMatrix(rowindexset, jb, je, M);
try {
check(M.minus(B.getMatrix(rowindexset, jb, je)), M);
try_success("setMatrix(int[],int,int,Matrix)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int,int,Matrix)... ",
"submatrix not successfully set");
}
B.setMatrix(ib, ie, jb, je, SUB);
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int,int,Matrix)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
try {
B.setMatrix(rowindexset, badcolumnindexset, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e) {
try {
B.setMatrix(badrowindexset, columnindexset, M);
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
try_success("setMatrix(int[],int[],Matrix)... ArrayIndexOutOfBoundsException... ", "");
}
} catch (java.lang.IllegalArgumentException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int[],Matrix)... ",
"ArrayIndexOutOfBoundsException expected but not thrown");
}
try {
B.setMatrix(rowindexset, columnindexset, M);
try {
check(M.minus(B.getMatrix(rowindexset, columnindexset)), M);
try_success("setMatrix(int[],int[],Matrix)... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "setMatrix(int[],int[],Matrix)... ", "submatrix not successfully set");
}
} catch (java.lang.ArrayIndexOutOfBoundsException e1) {
errorCount =
try_failure(
errorCount,
"setMatrix(int[],int[],Matrix)... ",
"Unexpected ArrayIndexOutOfBoundsException");
}
/**
* Array-like methods: minus minusEquals plus plusEquals arrayLeftDivide arrayLeftDivideEquals
* arrayRightDivide arrayRightDivideEquals arrayTimes arrayTimesEquals uminus
*/
print("\nTesting array-like methods...\n");
S = new Matrix(columnwise, nonconformld);
R = Matrix.random(A.getRowDimension(), A.getColumnDimension());
A = R;
try {
S = A.minus(S);
errorCount =
try_failure(errorCount, "minus conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("minus conformance check... ", "");
}
if (A.minus(R).norm1() != 0.) {
errorCount =
try_failure(
errorCount,
"minus... ",
"(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)");
} else {
try_success("minus... ", "");
}
A = R.copy();
A.minusEquals(R);
Z = new Matrix(A.getRowDimension(), A.getColumnDimension());
try {
A.minusEquals(S);
errorCount =
try_failure(errorCount, "minusEquals conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("minusEquals conformance check... ", "");
}
if (A.minus(Z).norm1() != 0.) {
errorCount =
try_failure(
errorCount,
"minusEquals... ",
"(difference of identical Matrices is nonzero,\nSubsequent use of minus should be suspect)");
} else {
try_success("minusEquals... ", "");
}
A = R.copy();
B = Matrix.random(A.getRowDimension(), A.getColumnDimension());
C = A.minus(B);
try {
S = A.plus(S);
errorCount =
try_failure(errorCount, "plus conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("plus conformance check... ", "");
}
try {
check(C.plus(B), A);
try_success("plus... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "plus... ", "(C = A - B, but C + B != A)");
}
C = A.minus(B);
C.plusEquals(B);
try {
A.plusEquals(S);
errorCount =
try_failure(errorCount, "plusEquals conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("plusEquals conformance check... ", "");
}
try {
check(C, A);
try_success("plusEquals... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "plusEquals... ", "(C = A - B, but C = C + B != A)");
}
A = R.uminus();
try {
check(A.plus(R), Z);
try_success("uminus... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "uminus... ", "(-A + A != zeros)");
}
A = R.copy();
O = new Matrix(A.getRowDimension(), A.getColumnDimension(), 1.0);
C = A.arrayLeftDivide(R);
try {
S = A.arrayLeftDivide(S);
errorCount =
try_failure(
errorCount, "arrayLeftDivide conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayLeftDivide conformance check... ", "");
}
try {
check(C, O);
try_success("arrayLeftDivide... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "arrayLeftDivide... ", "(M.\\M != ones)");
}
try {
A.arrayLeftDivideEquals(S);
errorCount =
try_failure(
errorCount,
"arrayLeftDivideEquals conformance check... ",
"nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayLeftDivideEquals conformance check... ", "");
}
A.arrayLeftDivideEquals(R);
try {
check(A, O);
try_success("arrayLeftDivideEquals... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "arrayLeftDivideEquals... ", "(M.\\M != ones)");
}
A = R.copy();
try {
A.arrayRightDivide(S);
errorCount =
try_failure(
errorCount, "arrayRightDivide conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayRightDivide conformance check... ", "");
}
C = A.arrayRightDivide(R);
try {
check(C, O);
try_success("arrayRightDivide... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "arrayRightDivide... ", "(M./M != ones)");
}
try {
A.arrayRightDivideEquals(S);
errorCount =
try_failure(
errorCount,
"arrayRightDivideEquals conformance check... ",
"nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayRightDivideEquals conformance check... ", "");
}
A.arrayRightDivideEquals(R);
try {
check(A, O);
try_success("arrayRightDivideEquals... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "arrayRightDivideEquals... ", "(M./M != ones)");
}
A = R.copy();
B = Matrix.random(A.getRowDimension(), A.getColumnDimension());
try {
S = A.arrayTimes(S);
errorCount =
try_failure(errorCount, "arrayTimes conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayTimes conformance check... ", "");
}
C = A.arrayTimes(B);
try {
check(C.arrayRightDivideEquals(B), A);
try_success("arrayTimes... ", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "arrayTimes... ", "(A = R, C = A.*B, but C./B != A)");
}
try {
A.arrayTimesEquals(S);
errorCount =
try_failure(
errorCount, "arrayTimesEquals conformance check... ", "nonconformance not raised");
} catch (IllegalArgumentException e) {
try_success("arrayTimesEquals conformance check... ", "");
}
A.arrayTimesEquals(B);
try {
check(A.arrayRightDivideEquals(B), R);
try_success("arrayTimesEquals... ", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "arrayTimesEquals... ", "(A = R, A = A.*B, but A./B != R)");
}
/** I/O methods: read print serializable: writeObject readObject */
print("\nTesting I/O methods...\n");
try {
DecimalFormat fmt = new DecimalFormat("0.0000E00");
fmt.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US));
PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out"));
A.print(FILE, fmt, 10);
FILE.close();
R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out")));
if (A.minus(R).norm1() < .001) {
try_success("print()/read()...", "");
} else {
errorCount =
try_failure(
errorCount,
"print()/read()...",
"Matrix read from file does not match Matrix printed to file");
}
} catch (java.io.IOException ioe) {
warningCount =
try_warning(
warningCount,
"print()/read()...",
"unexpected I/O error, unable to run print/read test; check write permission in current directory and retry");
} catch (Exception e) {
try {
e.printStackTrace(System.out);
warningCount =
try_warning(
warningCount,
"print()/read()...",
"Formatting error... will try JDK1.1 reformulation...");
DecimalFormat fmt = new DecimalFormat("0.0000");
PrintWriter FILE = new PrintWriter(new FileOutputStream("JamaTestMatrix.out"));
A.print(FILE, fmt, 10);
FILE.close();
R = Matrix.read(new BufferedReader(new FileReader("JamaTestMatrix.out")));
if (A.minus(R).norm1() < .001) {
try_success("print()/read()...", "");
} else {
errorCount =
try_failure(
errorCount,
"print()/read() (2nd attempt) ...",
"Matrix read from file does not match Matrix printed to file");
}
} catch (java.io.IOException ioe) {
warningCount =
try_warning(
warningCount,
"print()/read()...",
"unexpected I/O error, unable to run print/read test; check write permission in current directory and retry");
}
}
R = Matrix.random(A.getRowDimension(), A.getColumnDimension());
String tmpname = "TMPMATRIX.serial";
try {
@SuppressWarnings("resource")
ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream(tmpname));
out.writeObject(R);
@SuppressWarnings("resource")
ObjectInputStream sin = new ObjectInputStream(new FileInputStream(tmpname));
A = (Matrix) sin.readObject();
try {
check(A, R);
try_success("writeObject(Matrix)/readObject(Matrix)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"writeObject(Matrix)/readObject(Matrix)...",
"Matrix not serialized correctly");
}
} catch (java.io.IOException ioe) {
warningCount =
try_warning(
warningCount,
"writeObject()/readObject()...",
"unexpected I/O error, unable to run serialization test; check write permission in current directory and retry");
} catch (Exception e) {
errorCount =
try_failure(
errorCount,
"writeObject(Matrix)/readObject(Matrix)...",
"unexpected error in serialization test");
}
/**
* LA methods: transpose times cond rank det trace norm1 norm2 normF normInf solve
* solveTranspose inverse chol eig lu qr svd
*/
print("\nTesting linear algebra methods...\n");
A = new Matrix(columnwise, 3);
T = new Matrix(tvals);
T = A.transpose();
try {
check(A.transpose(), T);
try_success("transpose...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "transpose()...", "transpose unsuccessful");
}
A.transpose();
try {
check(A.norm1(), columnsummax);
try_success("norm1...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "norm1()...", "incorrect norm calculation");
}
try {
check(A.normInf(), rowsummax);
try_success("normInf()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "normInf()...", "incorrect norm calculation");
}
try {
check(A.normF(), Math.sqrt(sumofsquares));
try_success("normF...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "normF()...", "incorrect norm calculation");
}
try {
check(A.trace(), sumofdiagonals);
try_success("trace()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "trace()...", "incorrect trace calculation");
}
try {
check(A.getMatrix(0, A.getRowDimension() - 1, 0, A.getRowDimension() - 1).det(), 0.);
try_success("det()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "det()...", "incorrect determinant calculation");
}
SQ = new Matrix(square);
try {
check(A.times(A.transpose()), SQ);
try_success("times(Matrix)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "times(Matrix)...", "incorrect Matrix-Matrix product calculation");
}
try {
check(A.times(0.), Z);
try_success("times(double)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount, "times(double)...", "incorrect Matrix-scalar product calculation");
}
A = new Matrix(columnwise, 4);
QRDecomposition QR = A.qr();
R = QR.getR();
try {
check(A, QR.getQ().times(R));
try_success("QRDecomposition...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "QRDecomposition...", "incorrect QR decomposition calculation");
}
SingularValueDecomposition SVD = A.svd();
try {
check(A, SVD.getU().times(SVD.getS().times(SVD.getV().transpose())));
try_success("SingularValueDecomposition...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"SingularValueDecomposition...",
"incorrect singular value decomposition calculation");
}
DEF = new Matrix(rankdef);
try {
check(DEF.rank(), Math.min(DEF.getRowDimension(), DEF.getColumnDimension()) - 1);
try_success("rank()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "rank()...", "incorrect rank calculation");
}
B = new Matrix(condmat);
SVD = B.svd();
double[] singularvalues = SVD.getSingularValues();
try {
check(
B.cond(),
singularvalues[0]
/ singularvalues[Math.min(B.getRowDimension(), B.getColumnDimension()) - 1]);
try_success("cond()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "cond()...", "incorrect condition number calculation");
}
int n = A.getColumnDimension();
A = A.getMatrix(0, n - 1, 0, n - 1);
A.set(0, 0, 0.);
LUDecomposition LU = A.lu();
try {
check(A.getMatrix(LU.getPivot(), 0, n - 1), LU.getL().times(LU.getU()));
try_success("LUDecomposition...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "LUDecomposition...", "incorrect LU decomposition calculation");
}
X = A.inverse();
try {
check(A.times(X), Matrix.identity(3, 3));
try_success("inverse()...", "");
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "inverse()...", "incorrect inverse calculation");
}
O = new Matrix(SUB.getRowDimension(), 1, 1.0);
SOL = new Matrix(sqSolution);
SQ = SUB.getMatrix(0, SUB.getRowDimension() - 1, 0, SUB.getRowDimension() - 1);
try {
check(SQ.solve(SOL), O);
try_success("solve()...", "");
} catch (java.lang.IllegalArgumentException e1) {
errorCount = try_failure(errorCount, "solve()...", e1.getMessage());
} catch (java.lang.RuntimeException e) {
errorCount = try_failure(errorCount, "solve()...", e.getMessage());
}
A = new Matrix(pvals);
CholeskyDecomposition Chol = A.chol();
Matrix L = Chol.getL();
try {
check(A, L.times(L.transpose()));
try_success("CholeskyDecomposition...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"CholeskyDecomposition...",
"incorrect Cholesky decomposition calculation");
}
X = Chol.solve(Matrix.identity(3, 3));
try {
check(A.times(X), Matrix.identity(3, 3));
try_success("CholeskyDecomposition solve()...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"CholeskyDecomposition solve()...",
"incorrect Choleskydecomposition solve calculation");
}
EigenvalueDecomposition Eig = A.eig();
Matrix D = Eig.getD();
Matrix V = Eig.getV();
try {
check(A.times(V), V.times(D));
try_success("EigenvalueDecomposition (symmetric)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"EigenvalueDecomposition (symmetric)...",
"incorrect symmetric Eigenvalue decomposition calculation");
}
A = new Matrix(evals);
Eig = A.eig();
D = Eig.getD();
V = Eig.getV();
try {
check(A.times(V), V.times(D));
try_success("EigenvalueDecomposition (nonsymmetric)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(
errorCount,
"EigenvalueDecomposition (nonsymmetric)...",
"incorrect nonsymmetric Eigenvalue decomposition calculation");
}
try {
print("\nTesting Eigenvalue; If this hangs, we've failed\n");
Matrix bA = new Matrix(badeigs);
EigenvalueDecomposition bEig = bA.eig();
try_success("EigenvalueDecomposition (hang)...", "");
} catch (java.lang.RuntimeException e) {
errorCount =
try_failure(errorCount, "EigenvalueDecomposition (hang)...", "incorrect termination");
}
print("\nTestMatrix completed.\n");
print("Total errors reported: " + Integer.toString(errorCount) + "\n");
print("Total warnings reported: " + Integer.toString(warningCount) + "\n");
}
/*
* Performs affine adaptation
*/
boolean calcAffineAdaptation(
final FImage fimage, EllipticInterestPointData kpt, AbstractStructureTensorIPD ipd) {
// DisplayUtilities.createNamedWindow("warp", "Warped Image ROI",true);
Matrix transf = new Matrix(2, 3); // Transformation matrix
Point2dImpl c = new Point2dImpl(); // Transformed point
Point2dImpl p = new Point2dImpl(); // Image point
Matrix U = Matrix.identity(2, 2); // Normalization matrix
Matrix Mk = U.copy();
FImage img_roi, warpedImg = new FImage(1, 1);
float Qinv = 1, q, si = kpt.scale; // sd = 0.75f * si;
float kptSize = 2 * 3 * kpt.scale;
boolean divergence = false, convergence = false;
int i = 0;
// Coordinates in image
int py = (int) kpt.y;
int px = (int) kpt.x;
// Roi coordinates
int roix, roiy;
// Coordinates in U-trasformation
int cx = px;
int cy = py;
int cxPr = cx;
int cyPr = cy;
float radius = kptSize / 2 * 1.4f;
float half_width, half_height;
Rectangle roi;
// Affine adaptation
while (i <= 10 && !divergence && !convergence) {
// Transformation matrix
MatrixUtils.zero(transf);
transf.setMatrix(0, 1, 0, 1, U);
kpt.setTransform(U);
Rectangle boundingBox = new Rectangle();
double ac_b2 = U.det();
boundingBox.width = (float) Math.ceil(U.get(1, 1) / ac_b2 * 3 * si * 1.4);
boundingBox.height = (float) Math.ceil(U.get(0, 0) / ac_b2 * 3 * si * 1.4);
// Create window around interest point
half_width = Math.min((float) Math.min(fimage.width - px - 1, px), boundingBox.width);
half_height = Math.min((float) Math.min(fimage.height - py - 1, py), boundingBox.height);
if (half_width <= 0 || half_height <= 0) return divergence;
roix = Math.max(px - (int) boundingBox.width, 0);
roiy = Math.max(py - (int) boundingBox.height, 0);
roi = new Rectangle(roix, roiy, px - roix + half_width + 1, py - roiy + half_height + 1);
// create ROI
img_roi = fimage.extractROI(roi);
// Point within the ROI
p.x = px - roix;
p.y = py - roiy;
// Find coordinates of square's angles to find size of warped ellipse's bounding box
float u00 = (float) U.get(0, 0);
float u01 = (float) U.get(0, 1);
float u10 = (float) U.get(1, 0);
float u11 = (float) U.get(1, 1);
float minx = u01 * img_roi.height < 0 ? u01 * img_roi.height : 0;
float miny = u10 * img_roi.width < 0 ? u10 * img_roi.width : 0;
float maxx =
(u00 * img_roi.width > u00 * img_roi.width + u01 * img_roi.height
? u00 * img_roi.width
: u00 * img_roi.width + u01 * img_roi.height)
- minx;
float maxy =
(u11 * img_roi.width > u10 * img_roi.width + u11 * img_roi.height
? u11 * img_roi.height
: u10 * img_roi.width + u11 * img_roi.height)
- miny;
// Shift
transf.set(0, 2, -minx);
transf.set(1, 2, -miny);
if (maxx >= 2 * radius + 1 && maxy >= 2 * radius + 1) {
// Size of normalized window must be 2*radius
// Transformation
FImage warpedImgRoi;
FProjectionProcessor proc = new FProjectionProcessor();
proc.setMatrix(transf);
img_roi.accumulateWith(proc);
warpedImgRoi = proc.performProjection(0, (int) maxx, 0, (int) maxy, null);
// DisplayUtilities.displayName(warpedImgRoi.clone().normalise(), "warp");
// Point in U-Normalized coordinates
c = p.transform(U);
cx = (int) (c.x - minx);
cy = (int) (c.y - miny);
if (warpedImgRoi.height > 2 * radius + 1 && warpedImgRoi.width > 2 * radius + 1) {
// Cut around normalized patch
roix = (int) Math.max(cx - Math.ceil(radius), 0.0);
roiy = (int) Math.max(cy - Math.ceil(radius), 0.0);
roi =
new Rectangle(
roix,
roiy,
cx - roix + (float) Math.min(Math.ceil(radius), warpedImgRoi.width - cx - 1) + 1,
cy
- roiy
+ (float) Math.min(Math.ceil(radius), warpedImgRoi.height - cy - 1)
+ 1);
warpedImg = warpedImgRoi.extractROI(roi);
// Coordinates in cutted ROI
cx = cx - roix;
cy = cy - roiy;
} else {
warpedImg.internalAssign(warpedImgRoi);
}
if (logger.getLevel() == Level.DEBUG) {
displayCurrentPatch(
img_roi.clone().normalise(),
p.x,
p.y,
warpedImg.clone().normalise(),
cx,
cy,
U,
si * 3);
}
// Integration Scale selection
si = selIntegrationScale(warpedImg, si, new Pixel(cx, cy));
// Differentation scale selection
if (fastDifferentiationScale) {
ipd = selDifferentiationScaleFast(warpedImg, ipd, si, new Pixel(cx, cy));
} else {
ipd = selDifferentiationScale(warpedImg, ipd, si, new Pixel(cx, cy));
}
if (ipd.maxima.size() == 0) {
divergence = true;
continue;
}
// Spatial Localization
cxPr = cx; // Previous iteration point in normalized window
cyPr = cy;
//
// float cornMax = 0;
// for (int j = 0; j < 3; j++)
// {
// for (int t = 0; t < 3; t++)
// {
// float dx2 = Lxm2smooth.pixels[cyPr - 1 + j][cxPr - 1 + t];
// float dy2 = Lym2smooth.pixels[cyPr - 1 + j][cxPr - 1 + t];
// float dxy = Lxmysmooth.pixels[cyPr - 1 + j][cxPr - 1 + t];
// float det = dx2 * dy2 - dxy * dxy;
// float tr = dx2 + dy2;
// float cornerness = (float) (det - (0.04 * Math.pow(tr, 2)));
//
// if (cornerness > cornMax) {
// cornMax = cornerness;
// cx = cxPr - 1 + t;
// cy = cyPr - 1 + j;
// }
// }
// }
FValuePixel max = ipd.findMaximum(new Rectangle(cxPr - 1, cyPr - 1, 3, 3));
cx = max.x;
cy = max.y;
// Transform point in image coordinates
p.x = px;
p.y = py;
// Displacement vector
c.x = cx - cxPr;
c.y = cy - cyPr;
// New interest point location in image
p.translate(c.transform(U.inverse()));
px = (int) p.x;
py = (int) p.y;
q = calcSecondMomentSqrt(ipd, new Pixel(cx, cy), Mk);
float ratio = 1 - q;
// if ratio == 1 means q == 0 and one axes equals to 0
if (!Float.isNaN(ratio) && ratio != 1) {
// Update U matrix
U = U.times(Mk);
Matrix uVal, uV;
// EigenvalueDecomposition ueig = U.eig();
EigenValueVectorPair ueig = MatrixUtils.symmetricEig2x2(U);
uVal = ueig.getValues();
uV = ueig.getVectors();
Qinv = normMaxEval(U, uVal, uV);
// Keypoint doesn't converge
if (Qinv >= 6) {
logger.debug("QInverse too large, feature too edge like, affine divergence!");
divergence = true;
} else if (ratio <= 0.05) { // Keypoint converges
convergence = true;
// Set transformation matrix
MatrixUtils.zero(transf);
transf.setMatrix(0, 1, 0, 1, U);
// The order here matters, setTransform uses the x and y to calculate a new ellipse
kpt.x = px;
kpt.y = py;
kpt.scale = si;
kpt.setTransform(U);
kpt.score = max.value;
// ax1 = (float) (1 / Math.abs(uVal.get(1, 1)) * 3 * si);
// ax2 = (float) (1 / Math.abs(uVal.get(0, 0)) * 3 * si);
// phi = Math.atan(uV.get(1, 1) / uV.get(0, 1));
// kpt.axes = new Point2dImpl(ax1, ax2);
// kpt.phi = phi;
// kpt.centre = new Pixel(px, py);
// kpt.si = si;
// kpt.size = 2 * 3 * si;
} else {
radius = (float) (3 * si * 1.4);
}
} else {
logger.debug("QRatio was close to 0, affine divergence!");
divergence = true;
}
} else {
logger.debug("Window size has grown too fast, scale divergence!");
divergence = true;
}
++i;
}
if (!divergence && !convergence) {
logger.debug("Reached max iterations!");
}
return convergence;
}
public boolean calcNearPD(Matrix x) {
int n = x.getRowDimension();
Matrix X;
// Init local variables
double[] diagX0 = new double[n];
double[] d = new double[n];
Matrix D_S = new Matrix(n, n);
Matrix R = new Matrix(n, n);
Matrix Y = new Matrix(n, n);
EigenvalueDecomposition eig;
Matrix D_plus = new Matrix(n, n);
Matrix Q = new Matrix(n, n);
if (keepDiag) {
for (int i = 0; i < n; i++) {
diagX0[i] = x.get(i, i);
}
}
X = x.copy();
// Set iteration, convergence criteria
int iter = 0;
boolean converged = false;
double conv = Double.POSITIVE_INFINITY;
// Loop
while ((iter < maxit) & !converged) {
Y = X.copy();
// Dykstra correction
if (doDykstra) {
R = Y.minus(D_S);
}
// project onto PSD matrices X_k = P_S (R_k)
if (doDykstra) {
eig = R.eig();
} else {
eig = Y.eig();
}
d = eig.getRealEigenvalues();
Q = eig.getV();
// Get the maximum eigenvalue
double eigMax = Double.NEGATIVE_INFINITY;
for (int i = 0; i < n; i++) {
if (d[i] > eigMax) eigMax = d[i];
}
// compute the D_plus diagonal matricies
for (int i = 0; i < n; i++) {
double d_plus = Math.max(d[i], eigTol * eigMax);
D_plus.set(i, i, d_plus);
}
X = (Q.times(D_plus)).times(Q.transpose());
// Update Dykstra correction
if (doDykstra) D_S = X.minus(R);
// project onto symmetric and possibly 'given diag' matrices:
if (keepDiag) {
for (int i = 0; i < n; i++) {
X.set(i, i, diagX0[i]);
}
}
// update convergence and iteration values
conv = (Y.minus(X)).normInf() / Y.normInf();
iter = iter + 1;
// check convergence criteria
if (conv <= convTol) converged = true;
}
// Set solution local variables as globals
this.X = X;
this.conv = conv;
this.normF = (x.minus(X)).normF();
this.iter = iter;
this.eigVals = d;
return converged;
}
/**
* This method gets the computed matrix X which is nearest to that input
*
* @return - the nearest PD matrix to that input
*/
public Matrix getNearPD() {
return X.copy();
}