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;
  }
Beispiel #2
0
 /**
  * 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);
 }
Beispiel #3
0
  /**
   * 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();
  }
Beispiel #4
0
 @Override
 public CalcObject plus() {
   return new MatrixObject(matrix.copy());
 }
Beispiel #5
0
    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;
  }
Beispiel #8
0
  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;
  }
Beispiel #9
0
 /**
  * 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();
 }