Java tutorial
/* * Copyright (c) 2012 Diamond Light Source Ltd. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 * which accompanies this distribution, and is available at * http://www.eclipse.org/legal/epl-v10.html */ package uk.ac.diamond.scisoft.analysis.roi.fitting; import java.util.Arrays; import org.apache.commons.math3.analysis.solvers.BrentSolver; import org.apache.commons.math3.exception.MathIllegalArgumentException; import org.apache.commons.math3.exception.TooManyEvaluationsException; import org.eclipse.dawnsci.analysis.api.fitting.IConicSectionFitter; import org.eclipse.dawnsci.analysis.api.io.IDataHolder; import org.eclipse.dawnsci.analysis.dataset.impl.Dataset; import org.eclipse.dawnsci.analysis.dataset.impl.DatasetFactory; import org.eclipse.dawnsci.analysis.dataset.impl.DatasetUtils; import org.eclipse.dawnsci.analysis.dataset.impl.DoubleDataset; import org.eclipse.dawnsci.analysis.dataset.impl.Maths; import org.eclipse.dawnsci.analysis.dataset.impl.Random; import org.eclipse.dawnsci.analysis.dataset.roi.fitting.AngleDerivativeFunction; import org.eclipse.dawnsci.analysis.dataset.roi.fitting.EllipseFitter; import org.junit.Assert; import org.junit.Test; import uk.ac.diamond.scisoft.analysis.io.LoaderFactory; public class EllipseFitterTest { @Test public void testOrthoDist() { AngleDerivativeFunction angleDerivative = new AngleDerivativeFunction(); BrentSolver solver = new BrentSolver(); double a = 10.2; double b = 3.1; final double twopi = 2 * Math.PI; double alpha = twopi * 10. / 360; // 0 to 2 pi angleDerivative.setRadii(a, b); angleDerivative.setAngle(alpha); // final double ca = 0; // final double cb = b-0.5; final double Xc = -5.; // Math.cos(alpha)*ca + Math.sin(alpha)*cb; final double Yc = 5.5; //Math.sin(alpha)*ca + Math.cos(alpha)*cb; angleDerivative.setCoordinate(Xc, Yc); try { // find quadrant to use double p = Math.atan2(Yc, Xc); if (p < 0) p += twopi; p -= alpha; final double end; final double halfpi = 0.5 * Math.PI; p /= halfpi; end = Math.ceil(p) * halfpi; final double angle = solver.solve(100, angleDerivative, end - halfpi, end); // final double cos = Math.cos(angle); // final double sin = Math.sin(angle); Assert.assertEquals("Angle found is not close enough", 1.930, angle, 0.001); // double dx = a*cos + Xc; // double dy = b*sin + Yc; // // System.out.println("Bracket angle = " + Math.ceil(p)); // System.out.println("Delta angle = " + 180.*angle/Math.PI); // System.out.println(dx + ", " + dy); } catch (TooManyEvaluationsException e) { // TODO System.err.println(e); } catch (MathIllegalArgumentException e) { // TODO System.err.println(e); } } @Test public void testQuickEllipse() { checkGeneratedEllipse(20, 10, 344.2, 243.2, Math.PI * 0.23, 0.2, -12.3); for (int i = 1; i <= 10; i++) { System.out.println("i = " + i); checkGeneratedEllipse(100, 3, 8.0701e+02, 4.7593e+00, i * 0.002 * Math.PI, 1.2024e+03, 1.6759e+02); } } void checkGeneratedEllipse(int pts, double std, double... original) { Random.seed(1277); DoubleDataset theta; // theta = new DoubleDataset(new double[] {0.1, 0.2, 0.25, 0.33, 0.35, 0.37, 0.43, }); // theta = Random.rand(0, 2*Math.PI, pts); theta = (DoubleDataset) DatasetFactory.createLinearSpace(0, 2 * Math.PI, pts, Dataset.FLOAT64); Dataset[] coords = EllipseFitter.generateCoordinates(theta, original); Dataset x; Dataset y; // x = new DoubleDataset(new double[] {242.34, 188.08, 300.04, 188.90, 300.97, 103.80, 157.67, 141.81, 302.64, 266.58}); // y = new DoubleDataset(new double[] {-262.478, 147.192, -107.673, 136.293, -118.735, 217.387, 166.996, 192.521, -55.201, 17.826}); x = Maths.add(coords[0], Random.randn(0.0, std, theta.getShape())); y = Maths.add(coords[1], Random.randn(0.0, std, theta.getShape())); System.err.println(x.toString(true)); System.err.println(y.toString(true)); IConicSectionFitter fitter = new EllipseFitter(); fitter.algebraicFit(x, y); double[] result = fitter.getParameters(); double[] rtols = new double[] { 1.5e-1, 11.5e-1, 1.5e-1, 7, 2e-1 }; double[] atols = new double[] { 10, 10, 5 * Math.PI / 180, 10, 10 }; for (int i = 0; i < original.length; i++) { double err = Math.max(Math.abs(original[i] * rtols[i]), atols[i]); Assert.assertEquals("Algebraic fit: " + i, original[i], result[i], err); } System.err.println(Arrays.toString(original)); System.err.println(Arrays.toString(result)); fitter.geometricFit(x, y, result); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); for (int i = 0; i < original.length; i++) { double err = Math.max(Math.abs(original[i] * rtols[i]), atols[i]); Assert.assertEquals("Geometric fit: " + i, original[i], result[i], err); } } @Test public void testFit() throws Exception { String fileName = "testfiles/points.dat"; IDataHolder dh = LoaderFactory.getData(fileName); Dataset x = DatasetUtils.convertToDataset(dh.getDataset(0)); Dataset y = DatasetUtils.convertToDataset(dh.getDataset(1)); if (x == null || y == null) { Assert.fail("Could not load data from " + fileName); return; } IConicSectionFitter fitter = new EllipseFitter(); fitter.algebraicFit(x, y); System.out.println("Res: " + fitter.getRMS()); double[] result = fitter.getParameters(); System.err.println(Arrays.toString(result)); fitter.geometricFit(x, y, result); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); double mx = (Double) x.mean(); double my = (Double) y.mean(); double px = x.peakToPeak().doubleValue(); double py = y.peakToPeak().doubleValue(); x.isubtract(mx); y.isubtract(my); System.err.println("Means: " + mx + ", " + my + "; PtP: " + px + ", " + py); fitter.algebraicFit(x, y); System.out.println("Res: " + fitter.getRMS()); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); fitter.geometricFit(x, y, result); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); result[3] += mx; result[4] += my; System.err.println(Arrays.toString(result)); x.idivide(px); y.idivide(py); fitter.algebraicFit(x, y); System.out.println("Res: " + fitter.getRMS()); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); fitter.geometricFit(x, y, result); result = fitter.getParameters(); System.err.println(Arrays.toString(result)); result[3] += mx; result[4] += my; System.err.println(Arrays.toString(result)); } }