/**
* Computes the euclidean centroid, it may not be the formal centroid for different metrics but
* intuitively the average counts should provide a good cluster representative which is what this
* method intends to return
*
* @param pwmSet - Collection of pwms from which to compute the centroid0
* @return The euclidean centroid
* @throws IllegalArgumentException - When not all PWMs have the same dimension.
*/
public PositionWeightMatrix centroidOf(Collection<PositionWeightMatrix> pwmSet)
throws IllegalArgumentException {
Matrix centroidMatrix = null;
Iterator<PositionWeightMatrix> pwmIt = pwmSet.iterator();
if (pwmIt.hasNext()) {
PositionWeightMatrix first = pwmIt.next();
PositionWeightColumn firstCol = first.get(0);
centroidMatrix = new Matrix(firstCol.getAlphabetSize(), first.getNumCol());
addToCentroid(centroidMatrix, first);
}
while (pwmIt.hasNext()) {
PositionWeightMatrix pwm = pwmIt.next();
if (pwm.getNumCol() != centroidMatrix.getColumnDimension()) {
throw new IllegalArgumentException(
"Error computing centroid. All PWMs in set should have the same dimension");
}
addToCentroid(centroidMatrix, pwm);
}
centroidMatrix.times(1 / (double) pwmSet.size());
PositionWeightMatrix centroid = new PositionWeightMatrix("centroid");
for (int j = 0; j < centroidMatrix.getColumnDimension(); j++) {
centroid.addColumn(centroidMatrix.getColumn(j));
}
return centroid;
}
public static Matrix add1sRow(Matrix m) {
Matrix a = new Matrix(m.getRowDimension() + 1, m.getColumnDimension());
for (int i = 0; i < a.getColumnDimension(); i++) {
a.set(0, i, 1);
}
return a;
}
public static Matrix remove1stColumn(Matrix m) {
Matrix a = new Matrix(m.getRowDimension(), m.getColumnDimension() - 1);
for (int i = 0; i < a.getRowDimension(); i++) {
for (int j = 0; j < a.getColumnDimension(); j++) {
a.set(i, j, m.get(i, j + 1));
}
}
return a;
}
public static Matrix add1sColumn(Matrix m) {
Matrix a = new Matrix(m.getRowDimension(), m.getColumnDimension() + 1);
for (int i = 0; i < a.getRowDimension(); i++) {
a.set(i, 0, 1);
for (int j = 1; j < a.getColumnDimension(); j++) {
a.set(i, j, m.get(i, j - 1));
}
}
return a;
}
/**
* @param m Matrix with 2 rows, one column (2x1)
* @return Point with same coordinates as in Matrix
* @throws InvalidParameterException if the Matrix has wrong dimensions
*/
public static Point2d matrixToPoint(final Matrix m) throws InvalidParameterException {
if (m.getColumnDimension() != 1)
throw new InvalidParameterException(
"Circle.matrixToPoint: wrong number of columns: " + m.getColumnDimension());
if (m.getRowDimension() != 2)
throw new InvalidParameterException(
"Circle.matrixToPoint: wrong number of rows: " + m.getRowDimension());
Point2d point = new Point2d(m.get(0, 0), m.get(1, 0));
return point;
}
/**
* @param m Matrix with 2 rows, one column (2x1)
* @return Vector2d with same coordinates as in Matrix
* @throws InvalidParameterException if the Matrix has wrong dimensions
*/
public static Vector2d matrixToVector(final Matrix m) throws InvalidParameterException {
if (m.getColumnDimension() != 1)
throw new InvalidParameterException(
"Circle.matrixToPoint: wrong number of columns: " + m.getColumnDimension());
if (m.getRowDimension() != 2)
throw new InvalidParameterException(
"Circle.matrixToPoint: wrong number of rows: " + m.getRowDimension());
Vector2d vector = new Vector2d(m.get(0, 0), m.get(1, 0));
return vector;
}
/**
* 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();
}
public static Matrix addBotMatrix(Matrix a, Matrix b) {
Matrix c = new Matrix(a.getRowDimension() + b.getRowDimension(), a.getColumnDimension());
for (int i = 0; i < a.getRowDimension(); i++) {
for (int j = 0; j < a.getColumnDimension(); j++) {
c.set(i, j, a.get(i, j));
}
}
for (int i = 0; i < b.getRowDimension(); i++) {
for (int j = 0; j < b.getColumnDimension(); j++) {
c.set(i + a.getRowDimension(), j, b.get(i, j));
}
}
return c;
}
private static Matrix rotatedMatrix(Matrix m, Matrix r) {
Matrix translationMatrix = new Matrix(m.getRowDimension(), m.getColumnDimension());
for (int c = 0; c < translationMatrix.getColumnDimension(); c++) {
// T
// x
translationMatrix.set(0, c, 2.0);
// y
translationMatrix.set(1, c, 3.0);
// z
// translationMatrix.set(2, c, 2.0);
}
Matrix rotatedMatrix = r.times(m.minus(translationMatrix)).plus(translationMatrix);
return rotatedMatrix;
}
public static Matrix inverse(Matrix x) {
int rows = x.getRowDimension();
int cols = x.getColumnDimension();
if (rows < cols) {
Matrix result = inverse(x.transpose());
if (result != null) result = result.transpose();
return result;
}
SingularValueDecomposition svdX = new SingularValueDecomposition(x);
if (svdX.rank() < 1) return null;
double[] singularValues = svdX.getSingularValues();
double tol = Math.max(rows, cols) * singularValues[0] * MACHEPS;
double[] singularValueReciprocals = new double[singularValues.length];
for (int i = 0; i < singularValues.length; i++)
if (Math.abs(singularValues[i]) >= tol) singularValueReciprocals[i] = 1.0 / singularValues[i];
double[][] u = svdX.getU().getArray();
double[][] v = svdX.getV().getArray();
int min = Math.min(cols, u[0].length);
double[][] inverse = new double[cols][rows];
for (int i = 0; i < cols; i++)
for (int j = 0; j < u.length; j++)
for (int k = 0; k < min; k++)
inverse[i][j] += v[i][k] * singularValueReciprocals[k] * u[j][k];
return new Matrix(inverse);
}
public static double[] row(Matrix m, int i) {
double[] array = new double[m.getColumnDimension()];
for (int k = 0; k < array.length; k++) {
array[k] = m.get(i, k);
}
return array;
}
@Override
public String toResultString() {
StringBuilder result =
new StringBuilder(
Tools.getLineSeparator() + "Principal Components:" + Tools.getLineSeparator());
if (manualNumber) {
result.append("Number of Components: " + numberOfComponents + Tools.getLineSeparator());
} else {
result.append("Proportion Threshold: " + proportionThreshold + Tools.getLineSeparator());
}
for (int i = 0; i < vMatrix.getColumnDimension(); i++) {
result.append("PC " + (i + 1) + ": ");
for (int j = 0; j < attributeNames.length; j++) {
double value = vMatrix.get(i, j);
if (value > 0) {
result.append(" + ");
} else {
result.append(" - ");
}
result.append(Tools.formatNumber(Math.abs(value)) + " * " + attributeNames[j]);
}
result.append(Tools.getLineSeparator());
}
return result.toString();
}
/**
* One common task in machine learning is evaluating an algorithm’s accuracy. One way you can use
* the existing data is to take some portion, say 90%, to train the classifier. Then you’ll take
* the remaining 10% to test the classifier and see how accurate it is.
*
* @return
* @throws IOException
*/
public int classifyTest() throws IOException {
FileHelper fileHelper = new FileHelper(INPUT_FILE_NAME);
Matrix dataSet = fileHelper.getMatrix();
Matrix normMat = autoNormalize(dataSet);
int testSetLength = (int) (normMat.getRowDimension() * TEST_RATIO);
Matrix trainingSubmatrix =
normMat.getMatrix(
testSetLength, normMat.getRowDimension() - 1, 0, normMat.getColumnDimension() - 1);
List<Integer> classLabels = fileHelper.getClassLabels();
List<Integer> trainingClassLabels = classLabels.subList(testSetLength, classLabels.size());
int errorCount = 0;
for (int i = 0; i < testSetLength; i++) {
int classifierResult =
classify(normMat.getArray()[i], trainingSubmatrix, trainingClassLabels, K_NUMBER);
System.out.println(
String.format(
"The classifier came back with: %d, the real answer is: %d",
classifierResult, classLabels.get(i)));
if (classifierResult != classLabels.get(i)) {
errorCount++;
}
}
log.info("The total error rate is: " + errorCount / (float) testSetLength);
log.info("Error number: " + errorCount);
return errorCount;
}
protected void addToCentroid(Matrix m, PositionWeightMatrix pwm) {
for (int i = 0; i < m.getColumnDimension(); i++) {
PositionWeightColumn c = pwm.get(i);
for (int j = 0; j < m.getRowDimension(); j++) {
m.set(j, i, m.get(j, i) + c.getWeight(j));
}
}
}
/**
* Checks if a matrix contains NaN elements
*
* @param m - original matrix
* @return boolean
*/
public static boolean matrixHasNanElements(Matrix m) {
for (int i = 0; i < m.getRowDimension(); i++) {
for (int j = 0; j < m.getColumnDimension(); j++) {
if (Double.isNaN(m.get(i, j))) {
return true;
}
}
}
return false;
}
static void writeMat(BufferedWriter s, Matrix M) throws IOException {
final int r = M.getRowDimension();
final int c = M.getColumnDimension();
s.write(r + " " + c + " 0"); // type always 0 for java version as its
// ignored
final double[][] Mv = M.getArray();
for (int rr = 0; rr < r; rr++) for (int cc = 0; cc < c; cc++) s.write(Mv[rr][cc] + " ");
}
public static double getSumOfSquares(Matrix m) {
if (m.getColumnDimension() != 1) {
System.out.println("SumOFSquares only defined on vectors");
}
double sumOfSquares = 0.0;
double[] elements = m.getColumnPackedCopy();
for (int i = 0; i < elements.length; i++) {
sumOfSquares += elements[i] * elements[i];
}
return sumOfSquares;
}
/**
* Returns a matrix which contains on the diagonal the original elements, and zeros elsewhere
* Input must be a nxm matrix with n = m
*
* @param m - original matrix
* @return Matrix - the filtered matrix
*/
public static Matrix getRectangularDiagonalMatrix(Matrix m) {
if (m.getRowDimension() != m.getColumnDimension()) {
return null;
}
Matrix diag = new Matrix(m.getRowDimension(), m.getRowDimension());
for (int i = 0; i < m.getRowDimension(); i++) {
diag.set(i, i, m.get(i, i));
}
return diag;
}
/**
* Returns the product of all elements of a matrix (equivalent to Python's numpy.product(m))
*
* @param m - the input matrix
* @return double - the result
*/
public static double getMatrixAllElementsProduct(Matrix m) {
final int rows = m.getRowDimension();
final int cols = m.getColumnDimension();
double result = 1.0;
for (int i = 0; i < rows; i++) {
for (int j = 0; j < cols; j++) {
result *= m.get(i, j);
}
}
return result;
}
public static RealMatrix getRealMatrixFromJamaMatrix(Matrix m) {
final int rDim = m.getRowDimension();
final int cDim = m.getColumnDimension();
RealMatrix rm = new Array2DRowRealMatrix(rDim, cDim);
for (int i = 0; i < rDim; i++) {
for (int j = 0; j < cDim; j++) {
rm.setEntry(i, j, m.get(i, j));
}
}
return rm;
}
/** Gets the max score in a matrix m. */
private double getMaxScore(final Matrix m) {
final double blockingValue = (Double) settings.get(KEY_BLOCKING_VALUE);
double max = Double.NEGATIVE_INFINITY;
for (int i = 0; i < m.getRowDimension(); i++) {
for (int j = 0; j < m.getColumnDimension(); j++) {
if (m.get(i, j) > max && m.get(i, j) < blockingValue) {
max = m.get(i, j);
}
}
}
return max;
}
public Matrix autoNormalize(Matrix dataSet) {
double[] minVals = new double[dataSet.getColumnDimension()];
Arrays.fill(minVals, Double.MAX_VALUE);
double[] maxVals = new double[dataSet.getColumnDimension()];
Arrays.fill(maxVals, Double.MIN_VALUE);
for (int i = 0; i < dataSet.getRowDimension(); i++) {
for (int j = 0; j < dataSet.getColumnDimension(); j++) {
double el0 = dataSet.get(i, j);
if (el0 < minVals[j]) {
minVals[j] = el0;
}
if (el0 > maxVals[j]) {
maxVals[j] = el0;
}
}
}
Matrix minMx = arrayToMatrix(minVals, dataSet.getRowDimension());
Matrix maxMx = arrayToMatrix(maxVals, dataSet.getRowDimension());
Matrix range = maxMx.minus(minMx);
Matrix diff = dataSet.minus(minMx);
return diff.arrayRightDivide(range);
}
/**
* Returns a rows x columns matrix with reciprocal elements
*
* @param m - the input matrix
* @return Matrix - the result matrix
*/
public static Matrix getReciprocalMatrix(Matrix m) {
final int rows = m.getRowDimension();
final int cols = m.getColumnDimension();
Matrix resultM = new Matrix(rows, cols);
for (int i = 0; i < rows; i++) {
for (int j = 0; j < cols; j++) {
if (m.get(i, j) != 0.0) {
resultM.set(i, j, 1.0 / m.get(i, j));
} else {
resultM.set(i, j, 0.0);
}
}
}
return resultM;
}
public void multipleLinearRegression(Matrix datay, Matrix dataX, boolean interceptTerm) {
b0Term = interceptTerm;
if (interceptTerm) { // first column of X is filled with 1s if b_0 != 0
int row = dataX.getRowDimension();
int col = dataX.getColumnDimension();
Matrix B = new Matrix(row, col + 1);
Matrix ones = new Matrix(row, 1);
for (int i = 0; i < row; i++) ones.set(i, 0, 1.0);
B.setMatrix(0, row - 1, 0, 0, ones);
B.setMatrix(0, row - 1, 1, col, dataX);
multipleLinearRegression(datay, B);
} else {
multipleLinearRegression(datay, dataX);
}
}
public void multipleLinearRegression(String fileName, boolean interceptTerm) {
try {
BufferedReader reader = new BufferedReader(new FileReader(fileName));
Matrix data = Matrix.read(reader);
reader.close();
int rows = data.getRowDimension() - 1;
int cols = data.getColumnDimension() - 1;
Matrix indVar =
data.getMatrix(0, rows, 0, 0); // dataVowels(:,0) -> col 0 is the independent variable
data = data.getMatrix(0, rows, 1, cols); // dataVowels(:,1:cols) -> dependent variables
multipleLinearRegression(indVar, data, interceptTerm);
} catch (Exception e) {
throw new RuntimeException("Problem reading file " + fileName, e);
}
}
/**
* * multipleLinearRegression providing index numbers for the columns in fileName, index 0
* correspond to column 1
*
* @param fileName
* @param indVariable column number (index) of the independent variable
* @param c int[] column numbers array (indices) of dependent variables
* @param rowIni and rowEnd should be given from 0 - maxData-1
* @param interceptTerm
*/
public void multipleLinearRegression(
String fileName,
int indVariable,
int[] c,
String[] factors,
boolean interceptTerm,
int rowIni,
int rowEnd) {
try {
BufferedReader reader = new BufferedReader(new FileReader(fileName));
Matrix data = Matrix.read(reader);
reader.close();
int rows = data.getRowDimension() - 1;
int cols = data.getColumnDimension() - 1;
if (rowIni < 0 || rowIni > rows)
throw new RuntimeException(
"Problem reading file, rowIni=" + rowIni + " and number of rows in file=" + rows);
if (rowEnd < 0 || rowEnd > rows)
throw new RuntimeException(
"Problem reading file, rowIni=" + rowIni + " and number of rows in file=" + rows);
if (rowIni > rowEnd)
throw new RuntimeException(
"Problem reading file, rowIni < rowend" + rowIni + " < " + rowEnd);
Matrix indVar =
data.getMatrix(
rowIni,
rowEnd,
indVariable,
indVariable); // dataVowels(:,0) -> last col is the independent variable
data =
data.getMatrix(
rowIni, rowEnd,
c); // the dependent variables correspond to the column indices in c
multipleLinearRegression(indVar, data, interceptTerm);
} catch (Exception e) {
throw new RuntimeException("Problem reading file " + fileName, e);
}
}
public MyMatrix times(MyMatrix m) {
if (numCols() != m.numRows()) {
throw new RuntimeException("Invalid Matrix");
}
Matrix res = new Matrix(a.getRowDimension(), m.numCols());
for (int i = 0; i < res.getRowDimension(); i++) {
for (int j = 0; j < res.getColumnDimension(); j++) {
double[] aY = new double[numCols()];
double[] bX = new double[m.numRows()];
for (int n = 0; n < aY.length; n++) {
aY[n] = a.get(i, n);
}
for (int n = 0; n < bX.length; n++) {
bX[n] = m.get(n, j);
}
MyVector u = new MyVector(aY);
MyVector v = new MyVector(bX);
res.set(i, j, u.dot(v));
}
}
return new MyMatrix(res);
}
/**
* Given an activation 'act', joints angles and speed, compute the tension applied on every joint.
*
* @param act in [0,1]
* @param angles (rad)
* @param angSpeed (rad/s)
* @return Torque (1xnb_joint) for each joint.
*/
public Matrix computeTorque(Matrix act, Matrix angles, Matrix angSpeed) {
// longueur du muscle
_ln = computeLength(angles);
// vitesse du muscle
_vn = computeSpeed(angles, angSpeed);
// tension (force)
for (int col = 0; col < _tn.getColumnDimension(); col++) {
assert act.get(0, col) >= 0.0 : "_act < 0";
assert act.get(0, col) <= 1.0 : "_act > 1";
double t =
funA(act.get(0, col), _ln.get(0, col))
* (funFl(_ln.get(0, col)) * funFv(_ln.get(0, col), _vn.get(0, col))
+ funFp(_ln.get(0, col)));
_tn.set(0, col, t);
}
// Real tension
_t = _tn.arrayTimes(_sec).times(31.8);
// Torque
_cpl = _t.times(_mom);
return _cpl;
}
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");
}
public int cols() {
return matrix.getColumnDimension();
}