Examples with BrownianDiffusionFunction uk.ac.sussex.gdsc.smlm.ij.plugins.TrackPopulationAnalysis.BrownianDiffusionFunction used on opensource projects

Example 1 with BrownianDiffusionFunction

use of uk.ac.sussex.gdsc.smlm.ij.plugins.TrackPopulationAnalysis.BrownianDiffusionFunction in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysisTest method canComputeBrownianModelUsingFbmFunction.

@Test
void canComputeBrownianModelUsingFbmFunction() {
    final int size = 10;
    final DoubleDoubleBiPredicate test = TestHelper.doublesAreClose(1e-5);
    final double alpha = 1.0;
    for (final double t : new double[] { 0.8, 1, 1.2 }) {
        final BrownianDiffusionFunction f1 = new BrownianDiffusionFunction(size, t);
        final FbmDiffusionFunction f2 = new FbmDiffusionFunction(size, t);
        for (final double d : new double[] { 0.8, 0.9, 1, 1.1, 1.2 }) {
            for (final double s : new double[] { 2, 20 }) {
                // Check the value and Jacobian
                final RealVector point1 = new ArrayRealVector(new double[] { d, s, alpha }, false);
                final Pair<RealVector, RealMatrix> p1 = f1.value(point1);
                final double[] value1 = p1.getFirst().toArray();
                final RealVector point2 = new ArrayRealVector(new double[] { d, s, alpha }, false);
                final Pair<RealVector, RealMatrix> p2 = f2.value(point2);
                final double[] value2 = p2.getFirst().toArray();
                TestAssertions.assertArrayTest(value1, value2, test, "value");
                final double[] dfda1 = p1.getSecond().getColumn(0);
                final double[] dfdb1 = p1.getSecond().getColumn(1);
                final double[] dfda2 = p2.getSecond().getColumn(0);
                final double[] dfdb2 = p2.getSecond().getColumn(1);
                TestAssertions.assertArrayTest(dfda1, dfda2, test, "jacobian dfda");
                TestAssertions.assertArrayTest(dfdb1, dfdb2, test, "jacobian dfdb");
            }
        }
    }
}

Example 2 with BrownianDiffusionFunction

use of uk.ac.sussex.gdsc.smlm.ij.plugins.TrackPopulationAnalysis.BrownianDiffusionFunction in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysisTest method canComputeBrownianDiffusionFunction1.

@Test
void canComputeBrownianDiffusionFunction1() {
    final int size = 10;
    final double delta = 1e-6;
    final DoubleDoubleBiPredicate test = TestHelper.doublesAreClose(1e-5);
    for (final double t : new double[] { 0.8, 1, 1.2 }) {
        final MultivariateJacobianFunction f = new BrownianDiffusionFunction(size, t);
        for (final double d : new double[] { 0.8, 0.9, 1, 1.1, 1.2 }) {
            for (final double s : new double[] { 2, 20 }) {
                // Check the value and Jacobian
                final RealVector point = new ArrayRealVector(new double[] { d, s }, false);
                final Pair<RealVector, RealMatrix> p = f.value(point);
                final double[] value = p.getFirst().toArray();
                Assertions.assertEquals(size, value.length);
                for (int n = 1; n <= size; n++) {
                    // MSD = 4Dt * (n - 1/3) + 4s^2
                    final double msd = 4 * d * t * (n - 1.0 / 3) + 4 * s * s;
                    TestAssertions.assertTest(msd, value[n - 1], test, "value");
                }
                // Columns of the Jacobian
                final double[] dfda1 = p.getSecond().getColumn(0);
                final double[] dfdb1 = p.getSecond().getColumn(1);
                point.setEntry(0, d - delta);
                RealVector v1 = f.value(point).getFirst();
                point.setEntry(0, d + delta);
                RealVector v2 = f.value(point).getFirst();
                final double[] dfda = v2.subtract(v1).mapDivide(2 * delta).toArray();
                point.setEntry(0, d);
                point.setEntry(1, s - delta);
                v1 = f.value(point).getFirst();
                point.setEntry(1, s + delta);
                v2 = f.value(point).getFirst();
                final double[] dfdb = v2.subtract(v1).mapDivide(2 * delta).toArray();
                // Element-by-element relative error
                TestAssertions.assertArrayTest(dfda, dfda1, test, "jacobian dfda");
                TestAssertions.assertArrayTest(dfdb, dfdb1, test, "jacobian dfdb");
            }
        }
    }
}