Java Code Examples for org.apache.commons.math3.optim.PointVectorValuePair#getPoint()
The following examples show how to use
org.apache.commons.math3.optim.PointVectorValuePair#getPoint() .
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Example 1
| Source File: AbstractLeastSquaresOptimizerAbstractTest.java From astor with GNU General Public License v2.0 | 6 votes |
|
public void doTestStRD(final StatisticalReferenceDataset dataset,
final double errParams,
final double errParamsSd) {
final AbstractLeastSquaresOptimizer optimizer = createOptimizer();
final double[] w = new double[dataset.getNumObservations()];
Arrays.fill(w, 1);
final double[][] data = dataset.getData();
final double[] initial = dataset.getStartingPoint(0);
final StatisticalReferenceDataset.LeastSquaresProblem problem = dataset.getLeastSquaresProblem();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(data[1]),
new Weight(w),
new InitialGuess(initial));
final double[] actual = optimum.getPoint();
for (int i = 0; i < actual.length; i++) {
double expected = dataset.getParameter(i);
double delta = FastMath.abs(errParams * expected);
Assert.assertEquals(dataset.getName() + ", param #" + i,
expected, actual[i], delta);
}
}
Example 2
| Source File: AbstractLeastSquaresOptimizerAbstractTest.java From astor with GNU General Public License v2.0 | 6 votes |
|
public void doTestStRD(final StatisticalReferenceDataset dataset,
final double errParams,
final double errParamsSd) {
final AbstractLeastSquaresOptimizer optimizer = createOptimizer();
final double[] w = new double[dataset.getNumObservations()];
Arrays.fill(w, 1);
final double[][] data = dataset.getData();
final double[] initial = dataset.getStartingPoint(0);
final StatisticalReferenceDataset.LeastSquaresProblem problem = dataset.getLeastSquaresProblem();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(data[1]),
new Weight(w),
new InitialGuess(initial));
final double[] actual = optimum.getPoint();
for (int i = 0; i < actual.length; i++) {
double expected = dataset.getParameter(i);
double delta = FastMath.abs(errParams * expected);
Assert.assertEquals(dataset.getName() + ", param #" + i,
expected, actual[i], delta);
}
}
Example 3
| Source File: AbstractLeastSquaresOptimizerAbstractTest.java From astor with GNU General Public License v2.0 | 6 votes |
|
public void doTestStRD(final StatisticalReferenceDataset dataset,
final double errParams,
final double errParamsSd) {
final AbstractLeastSquaresOptimizer optimizer = createOptimizer();
final double[] w = new double[dataset.getNumObservations()];
Arrays.fill(w, 1);
final double[][] data = dataset.getData();
final double[] initial = dataset.getStartingPoint(0);
final StatisticalReferenceDataset.LeastSquaresProblem problem = dataset.getLeastSquaresProblem();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(data[1]),
new Weight(w),
new InitialGuess(initial));
final double[] actual = optimum.getPoint();
for (int i = 0; i < actual.length; i++) {
double expected = dataset.getParameter(i);
double delta = FastMath.abs(errParams * expected);
Assert.assertEquals(dataset.getName() + ", param #" + i,
expected, actual[i], delta);
}
}
Example 4
| Source File: AbstractLeastSquaresOptimizerAbstractTest.java From astor with GNU General Public License v2.0 | 6 votes |
|
public void doTestStRD(final StatisticalReferenceDataset dataset,
final double errParams,
final double errParamsSd) {
final AbstractLeastSquaresOptimizer optimizer = createOptimizer();
final double[] w = new double[dataset.getNumObservations()];
Arrays.fill(w, 1);
final double[][] data = dataset.getData();
final double[] initial = dataset.getStartingPoint(0);
final StatisticalReferenceDataset.LeastSquaresProblem problem = dataset.getLeastSquaresProblem();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(data[1]),
new Weight(w),
new InitialGuess(initial));
final double[] actual = optimum.getPoint();
for (int i = 0; i < actual.length; i++) {
double expected = dataset.getParameter(i);
double delta = FastMath.abs(errParams * expected);
Assert.assertEquals(dataset.getName() + ", param #" + i,
expected, actual[i], delta);
}
}
Example 5
| Source File: AbstractLeastSquaresOptimizerAbstractTest.java From astor with GNU General Public License v2.0 | 6 votes |
|
public void doTestStRD(final StatisticalReferenceDataset dataset,
final double errParams,
final double errParamsSd) {
final AbstractLeastSquaresOptimizer optimizer = createOptimizer();
final double[] w = new double[dataset.getNumObservations()];
Arrays.fill(w, 1);
final double[][] data = dataset.getData();
final double[] initial = dataset.getStartingPoint(0);
final StatisticalReferenceDataset.LeastSquaresProblem problem = dataset.getLeastSquaresProblem();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(data[1]),
new Weight(w),
new InitialGuess(initial));
final double[] actual = optimum.getPoint();
for (int i = 0; i < actual.length; i++) {
double expected = dataset.getParameter(i);
double delta = FastMath.abs(errParams * expected);
Assert.assertEquals(dataset.getName() + ", param #" + i,
expected, actual[i], delta);
}
}
Example 6
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum = optimizer.optimize(new MaxEval(100),
circle.getModelFunction(),
circle.getModelFunctionJacobian(),
new Target(circle.target()),
new Weight(circle.weight()),
new InitialGuess(init));
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 7
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum = optimizer.optimize(new MaxEval(100),
circle.getModelFunction(),
circle.getModelFunctionJacobian(),
new Target(circle.target()),
new Weight(circle.weight()),
new InitialGuess(init));
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 8
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(dataPoints[1]),
new Weight(weights),
new InitialGuess(new double[] { 10, 900, 80, 27, 225 }));
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 9
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum = optimizer.optimize(new MaxEval(100),
circle.getModelFunction(),
circle.getModelFunctionJacobian(),
new Target(circle.target()),
new Weight(circle.weight()),
new InitialGuess(init));
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 10
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(dataPoints[1]),
new Weight(weights),
new InitialGuess(new double[] { 10, 900, 80, 27, 225 }));
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 11
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer = LevenbergMarquardtOptimizer.create()
.withMaxEvaluations(100)
.withMaxIterations(50)
.withModelAndJacobian(circle.getModelFunction(),
circle.getModelFunctionJacobian())
.withTarget(circle.target())
.withWeight(new DiagonalMatrix(circle.weight()))
.withStartPoint(init);
final PointVectorValuePair optimum = optimizer.optimize();
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 12
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer = LevenbergMarquardtOptimizer.create()
.withMaxEvaluations(100)
.withMaxIterations(20)
.withModelAndJacobian(problem.getModelFunction(),
problem.getModelFunctionJacobian())
.withTarget(dataPoints[1])
.withWeight(new DiagonalMatrix(weights))
.withStartPoint(new double[] { 10, 900, 80, 27, 225 });
final PointVectorValuePair optimum = optimizer.optimize();
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 13
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(dataPoints[1]),
new Weight(weights),
new InitialGuess(new double[] { 10, 900, 80, 27, 225 }));
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 14
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(dataPoints[1]),
new Weight(weights),
new InitialGuess(new double[] { 10, 900, 80, 27, 225 }));
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 15
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum = optimizer.optimize(new MaxEval(100),
circle.getModelFunction(),
circle.getModelFunctionJacobian(),
new Target(circle.target()),
new Weight(circle.weight()),
new InitialGuess(init));
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 16
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum
= optimizer.optimize(new MaxEval(100),
problem.getModelFunction(),
problem.getModelFunctionJacobian(),
new Target(dataPoints[1]),
new Weight(weights),
new InitialGuess(new double[] { 10, 900, 80, 27, 225 }));
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 17
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer = LevenbergMarquardtOptimizer.create()
.withMaxEvaluations(100)
.withMaxIterations(50)
.withModelAndJacobian(circle.getModelFunction(),
circle.getModelFunctionJacobian())
.withTarget(circle.target())
.withWeight(new DiagonalMatrix(circle.weight()))
.withStartPoint(init);
final PointVectorValuePair optimum = optimizer.optimize();
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
Example 18
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
/**
* Non-linear test case: fitting of decay curve (from Chapter 8 of
* Bevington's textbook, "Data reduction and analysis for the physical sciences").
* XXX The expected ("reference") values may not be accurate and the tolerance too
* relaxed for this test to be currently really useful (the issue is under
* investigation).
*/
@Test
public void testBevington() {
final double[][] dataPoints = {
// column 1 = times
{ 15, 30, 45, 60, 75, 90, 105, 120, 135, 150,
165, 180, 195, 210, 225, 240, 255, 270, 285, 300,
315, 330, 345, 360, 375, 390, 405, 420, 435, 450,
465, 480, 495, 510, 525, 540, 555, 570, 585, 600,
615, 630, 645, 660, 675, 690, 705, 720, 735, 750,
765, 780, 795, 810, 825, 840, 855, 870, 885, },
// column 2 = measured counts
{ 775, 479, 380, 302, 185, 157, 137, 119, 110, 89,
74, 61, 66, 68, 48, 54, 51, 46, 55, 29,
28, 37, 49, 26, 35, 29, 31, 24, 25, 35,
24, 30, 26, 28, 21, 18, 20, 27, 17, 17,
14, 17, 24, 11, 22, 17, 12, 10, 13, 16,
9, 9, 14, 21, 17, 13, 12, 18, 10, },
};
final BevingtonProblem problem = new BevingtonProblem();
final int len = dataPoints[0].length;
final double[] weights = new double[len];
for (int i = 0; i < len; i++) {
problem.addPoint(dataPoints[0][i],
dataPoints[1][i]);
weights[i] = 1 / dataPoints[1][i];
}
final LevenbergMarquardtOptimizer optimizer = LevenbergMarquardtOptimizer.create()
.withMaxEvaluations(100)
.withMaxIterations(20)
.withModelAndJacobian(problem.getModelFunction(),
problem.getModelFunctionJacobian())
.withTarget(dataPoints[1])
.withWeight(new DiagonalMatrix(weights))
.withStartPoint(new double[] { 10, 900, 80, 27, 225 });
final PointVectorValuePair optimum = optimizer.optimize();
final double[] solution = optimum.getPoint();
final double[] expectedSolution = { 10.4, 958.3, 131.4, 33.9, 205.0 };
final double[][] covarMatrix = optimizer.computeCovariances(solution, 1e-14);
final double[][] expectedCovarMatrix = {
{ 3.38, -3.69, 27.98, -2.34, -49.24 },
{ -3.69, 2492.26, 81.89, -69.21, -8.9 },
{ 27.98, 81.89, 468.99, -44.22, -615.44 },
{ -2.34, -69.21, -44.22, 6.39, 53.80 },
{ -49.24, -8.9, -615.44, 53.8, 929.45 }
};
final int numParams = expectedSolution.length;
// Check that the computed solution is within the reference error range.
for (int i = 0; i < numParams; i++) {
final double error = FastMath.sqrt(expectedCovarMatrix[i][i]);
Assert.assertEquals("Parameter " + i, expectedSolution[i], solution[i], error);
}
// Check that each entry of the computed covariance matrix is within 10%
// of the reference matrix entry.
for (int i = 0; i < numParams; i++) {
for (int j = 0; j < numParams; j++) {
Assert.assertEquals("Covariance matrix [" + i + "][" + j + "]",
expectedCovarMatrix[i][j],
covarMatrix[i][j],
FastMath.abs(0.1 * expectedCovarMatrix[i][j]));
}
}
}
Example 19
| Source File: LevenbergMarquardtOptimizerTest.java From astor with GNU General Public License v2.0 | 4 votes |
|
@Test
public void testCircleFitting2() {
final double xCenter = 123.456;
final double yCenter = 654.321;
final double xSigma = 10;
final double ySigma = 15;
final double radius = 111.111;
// The test is extremely sensitive to the seed.
final long seed = 59421061L;
final RandomCirclePointGenerator factory
= new RandomCirclePointGenerator(xCenter, yCenter, radius,
xSigma, ySigma,
seed);
final CircleProblem circle = new CircleProblem(xSigma, ySigma);
final int numPoints = 10;
for (Vector2D p : factory.generate(numPoints)) {
circle.addPoint(p.getX(), p.getY());
}
// First guess for the center's coordinates and radius.
final double[] init = { 90, 659, 115 };
final LevenbergMarquardtOptimizer optimizer
= new LevenbergMarquardtOptimizer();
final PointVectorValuePair optimum = optimizer.optimize(new MaxEval(100),
circle.getModelFunction(),
circle.getModelFunctionJacobian(),
new Target(circle.target()),
new Weight(circle.weight()),
new InitialGuess(init));
final double[] paramFound = optimum.getPoint();
// Retrieve errors estimation.
final double[] asymptoticStandardErrorFound = optimizer.computeSigma(paramFound, 1e-14);
// Check that the parameters are found within the assumed error bars.
Assert.assertEquals(xCenter, paramFound[0], asymptoticStandardErrorFound[0]);
Assert.assertEquals(yCenter, paramFound[1], asymptoticStandardErrorFound[1]);
Assert.assertEquals(radius, paramFound[2], asymptoticStandardErrorFound[2]);
}
