Examples of Jama.Matrix

Jama.Matrix
Jama = Java Matrix class.
The Java Matrix Class provides the fundamental operations of numerical linear algebra. Various constructors create Matrices from two dimensional arrays of double precision floating point numbers. Various "gets" and "sets" provide access to submatrices and matrix elements. Several methods implement basic matrix arithmetic, including matrix addition and multiplication, matrix norms, and element-by-element array operations. Methods for reading and printing matrices are also included. All the operations in this version of the Matrix Class involve real matrices. Complex matrices may be handled in a future version.
Five fundamental matrix decompositions, which consist of pairs or triples of matrices, permutation vectors, and the like, produce results in five decomposition classes. These decompositions are accessed by the Matrix class to compute solutions of simultaneous linear equations, determinants, inverses and other matrix functions. The five decompositions are:
- Cholesky Decomposition of symmetric, positive definite matrices.
- LU Decomposition of rectangular matrices.
- QR Decomposition of rectangular matrices.
- Singular Value Decomposition of rectangular matrices.
- Eigenvalue Decomposition of both symmetric and nonsymmetric square matrices.
Example of use:
Solve a linear system A x = b and compute the residual norm, ||b - A x||.
```
 double[][] vals = {{1.,2.,3},{4.,5.,6.},{7.,8.,10.}}; Matrix A = new Matrix(vals); Matrix b = Matrix.random(3,1); Matrix x = A.solve(b); Matrix r = A.times(x).minus(b); double rnorm = r.normInf(); 
```
@author The MathWorks, Inc. and the National Institute of Standards and Technology. @version 5 August 1998

 substantial problem within the implementation that was not anticipated in the test design.  
 The stopping point should give an indication of where the problem exists.
 **/
public class TestMatrix {
    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 = { { 1., 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.}};
        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 {
            ObjectOutputStream out = new ObjectOutputStream(
                    new FileOutputStream(tmpname));


            out.writeObject(R);
            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");

View Full Code Here

    }


    /** Check norm of difference of arrays. **/


    private static void check(double[][] x, double[][] y) {
        Matrix A = new Matrix(x);
        Matrix B = new Matrix(y);


        check(A, B);
    }

View Full Code Here

    /** Print a row vector. **/


    private static void print(double[] x, int w, int d) {
        // Use format Fw.d for all elements.
        System.out.print("\n");
        new Matrix(x, 1).print(w, d);
        print("\n");
    }

View Full Code Here

            // Singly Even Order


        } else {
            int p = n / 2;
            int k = (n - 2) / 4;
            Matrix A = magic(p);


            for (int j = 0; j < p; j++) {
                for (int i = 0; i < p; i++) {
                    double aij = A.get(i, j);


                    M[i][j] = aij;
                    M[i][j + p] = aij + 2 * p * p;
                    M[i + p][j] = aij + 3 * p * p;
                    M[i + p][j + p] = aij + p * p;
                }
            }
            for (int i = 0; i < p; i++) {
                for (int j = 0; j < k; j++) {
                    double t = M[i][j];


                    M[i][j] = M[i + p][j];
                    M[i + p][j] = t;
                }
                for (int j = n - k + 1; j < n; j++) {
                    double t = M[i][j];


                    M[i][j] = M[i + p][j];
                    M[i + p][j] = t;
                }
            }
            double t = M[k][0];


            M[k][0] = M[k + p][0];
            M[k + p][0] = t;
            t = M[k][k];
            M[k][k] = M[k + p][k];
            M[k + p][k] = t;
        }
        return new Matrix(M);
    }

View Full Code Here

        double eps = Math.pow(2.0, -52.0);


        for (int n = 3; n <= 32; n++) {
            print(fixedWidthIntegertoString(n, 7));


            Matrix M = magic(n);


            int t = (int) M.trace();


            print(fixedWidthIntegertoString(t, 10));


            EigenvalueDecomposition E = new EigenvalueDecomposition(
                    M.plus(M.transpose()).times(0.5));
            double[] d = E.getRealEigenvalues();


            print(fixedWidthDoubletoString(d[n - 1], 14, 3));


            int r = M.rank();


            print(fixedWidthIntegertoString(r, 7));


            double c = M.cond();


            print(
                    c < 1 / eps
                            ? fixedWidthDoubletoString(c, 12, 3)
                            : "         Inf");


            LUDecomposition LU = new LUDecomposition(M);
            Matrix L = LU.getL();
            Matrix U = LU.getU();
            int[] p = LU.getPivot();
            Matrix R = L.times(U).minus(M.getMatrix(p, 0, n - 1));
            double res = R.norm1() / (n * eps);


            print(fixedWidthDoubletoString(res, 12, 3));


            QRDecomposition QR = new QRDecomposition(M);
            Matrix Q = QR.getQ();


            R = QR.getR();
            R = Q.times(R).minus(M);
            res = R.norm1() / (n * eps);
            print(fixedWidthDoubletoString(res, 12, 3));


            print("\n");
        }

View Full Code Here

        }
    }


    @Override
  public double getProb(List args, Object value) {
        Matrix v = getParentVector(args);


        if (value instanceof Matrix) {
            MultivarGaussian distrib = new MultivarGaussian(mu.plus(W.times(v)),
                    Sigma);

View Full Code Here

        return 0;
    }


    @Override
  public Object sampleVal(List args) {
        Matrix v = getParentVector(args);
        MultivarGaussian distrib = new MultivarGaussian(mu.plus(W.times(v)),
                Sigma);


        return distrib.sampleVal();
    }

View Full Code Here


        return distrib.sampleVal();
    }


    private Matrix getParentVector(List args) {
        Matrix v = new Matrix(c, 1);
        int curRow = 0;


        for (Iterator iter = args.iterator(); iter.hasNext();) {
            Object arg = iter.next();


            if (!((arg instanceof Matrix)
                    && (((Matrix) arg).getColumnDimension() == 1))) {
                throw new IllegalArgumentException(
                        "Arguments for LinearGaussian CPD must be "
                                + "column vectors.");
            }


            Matrix parent = (Matrix) arg;


            if (curRow + parent.getRowDimension() > c) {
                throw new IllegalArgumentException(
                        "Error in LinearGaussian CPD: sum of dimensions of "
                                + "parents exceeds number of columns in W.");
            }
            v.setMatrix(curRow, curRow + parent.getRowDimension() - 1, 0, 0,
                    parent);
            curRow += parent.getRowDimension();
        }


        if (curRow < c) {
            throw new IllegalArgumentException(
                    "Error in LinearGaussian CPD: sum of dimensions of "

View Full Code Here

     * was constructed with a fixed mean and covariance matrix (internal 
     * calls are ok if the private method <code>initParams</code> is called 
     * first). 
     */
    public Matrix sampleVal() {
        Matrix temp = new Matrix(d, 1);


        for (int i = 0; i < d; i++) {
            temp.set(i, 0, UnivarGaussian.STANDARD.sampleVal());
        }
        return mu.plus(sqrtSigma.times(temp));
    }

View Full Code Here

     */
    public void iteration() {
        final int rowCount = trainingData.size();
        final int inputColCount = trainingData.get(0).getInput().length;


        final Matrix xMatrix = new Matrix(rowCount, inputColCount + 1);
        final Matrix yMatrix = new Matrix(rowCount, 1);


        for (int row = 0; row < trainingData.size(); row++) {
            final BasicData dataRow = this.trainingData.get(row);
            final int colSize = dataRow.getInput().length;


            xMatrix.set(row, 0, 1);
            for (int col = 0; col < colSize; col++) {
                xMatrix.set(row, col + 1, dataRow.getInput()[col]);
            }
            yMatrix.set(row, 0, dataRow.getIdeal()[0]);
        }


        // Calculate the least squares solution
        final QRDecomposition qr = new QRDecomposition(xMatrix);
        final Matrix beta = qr.solve(yMatrix);


        double sum = 0.0;
        for (int i = 0; i < inputColCount; i++)
            sum += yMatrix.get(i, 0);
        final double mean = sum / inputColCount;


        for (int i = 0; i < inputColCount; i++) {
            final double dev = yMatrix.get(i, 0) - mean;
            sst += dev * dev;
        }


        final Matrix residuals = xMatrix.times(beta).minus(yMatrix);
        sse = residuals.norm2() * residuals.norm2();


        for (int i = 0; i < this.algorithm.getLongTermMemory().length; i++) {
            this.algorithm.getLongTermMemory()[i] = beta.get(i, 0);
        }

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