Examples with SeededTest uk.ac.sussex.gdsc.test.junit5.SeededTest used on opensource projects

Example 51 with SeededTest

use of uk.ac.sussex.gdsc.test.junit5.SeededTest in project GDSC-SMLM by aherbert.

the class FastMleGradient2ProcedureTest method gradientProcedureComputesSameWithPrecomputed.

@SeededTest
void gradientProcedureComputesSameWithPrecomputed(RandomSeed seed) {
    final int iter = 10;
    final UniformRandomProvider rng = RngUtils.create(seed.getSeed());
    final ErfGaussian2DFunction f1 = (ErfGaussian2DFunction) GaussianFunctionFactory.create2D(1, 10, 10, GaussianFunctionFactory.FIT_ERF_FREE_CIRCLE, null);
    final ErfGaussian2DFunction f2 = (ErfGaussian2DFunction) GaussianFunctionFactory.create2D(2, 10, 10, GaussianFunctionFactory.FIT_ERF_FREE_CIRCLE, null);
    final double[] a1 = new double[1 + Gaussian2DFunction.PARAMETERS_PER_PEAK];
    final double[] a2 = new double[1 + 2 * Gaussian2DFunction.PARAMETERS_PER_PEAK];
    final double[] x = new double[f1.size()];
    final double[] b = new double[f1.size()];
    for (int i = 0; i < iter; i++) {
        final int ii = i;
        a2[Gaussian2DFunction.BACKGROUND] = nextUniform(rng, 0.1, 0.3);
        a2[Gaussian2DFunction.SIGNAL] = nextUniform(rng, 100, 300);
        a2[Gaussian2DFunction.X_POSITION] = nextUniform(rng, 3, 5);
        a2[Gaussian2DFunction.Y_POSITION] = nextUniform(rng, 3, 5);
        a2[Gaussian2DFunction.Z_POSITION] = nextUniform(rng, -2, 2);
        a2[Gaussian2DFunction.X_SD] = nextUniform(rng, 1, 1.3);
        a2[Gaussian2DFunction.Y_SD] = nextUniform(rng, 1, 1.3);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.SIGNAL] = nextUniform(rng, 100, 300);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.X_POSITION] = nextUniform(rng, 5, 7);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.Y_POSITION] = nextUniform(rng, 5, 7);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.Z_POSITION] = nextUniform(rng, -3, 1);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.X_SD] = nextUniform(rng, 1, 1.3);
        a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + Gaussian2DFunction.Y_SD] = nextUniform(rng, 1, 1.3);
        // Simulate Poisson data
        f2.initialise0(a2);
        f1.forEach(new ValueProcedure() {

            int index = 0;

            @Override
            public void execute(double value) {
                if (value > 0) {
                    x[index++] = GdscSmlmTestUtils.createPoissonSampler(rng, value).sample();
                } else {
                    x[index++] = 0;
                }
            }
        });
        // Precompute peak 2 (no background)
        a1[Gaussian2DFunction.BACKGROUND] = 0;
        for (int j = 1; j < 7; j++) {
            a1[j] = a2[Gaussian2DFunction.PARAMETERS_PER_PEAK + j];
        }
        f1.initialise0(a1);
        f1.forEach(new ValueProcedure() {

            int index = 0;

            @Override
            public void execute(double value) {
                b[index++] = value;
            }
        });
        // Reset to peak 1
        for (int j = 0; j < 7; j++) {
            a1[j] = a2[j];
        }
        // Compute peak 1+2
        final FastMleGradient2Procedure p12 = FastMleGradient2ProcedureUtils.create(x, f2);
        p12.computeSecondDerivative(a2);
        final double[] d11 = Arrays.copyOf(p12.d1, f1.getNumberOfGradients());
        final double[] d21 = Arrays.copyOf(p12.d2, f1.getNumberOfGradients());
        // Compute peak 1+(precomputed 2)
        final FastMleGradient2Procedure p1b2 = FastMleGradient2ProcedureUtils.create(x, OffsetGradient2Function.wrapGradient2Function(f1, b));
        p1b2.computeSecondDerivative(a1);
        final double[] d12 = p1b2.d1;
        final double[] d22 = p1b2.d2;
        Assertions.assertArrayEquals(p12.u, p1b2.u, 1e-10, () -> " Result: Not same @ " + ii);
        Assertions.assertArrayEquals(d11, d12, 1e-10, () -> " D1: Not same @ " + ii);
        Assertions.assertArrayEquals(d21, d22, 1e-10, () -> " D2: Not same @ " + ii);
        final double[] v1 = p12.computeValue(a2);
        final double[] v2 = p1b2.computeValue(a1);
        Assertions.assertArrayEquals(v1, v2, 1e-10, () -> " Value: Not same @ " + ii);
        final double[] d1 = Arrays.copyOf(p12.computeFirstDerivative(a2), f1.getNumberOfGradients());
        final double[] d2 = p1b2.computeFirstDerivative(a1);
        Assertions.assertArrayEquals(d1, d2, 1e-10, () -> " 1st derivative: Not same @ " + ii);
    }
}

Example 52 with SeededTest

use of uk.ac.sussex.gdsc.test.junit5.SeededTest in project GDSC-SMLM by aherbert.

the class OffsetFunctionTest method offsetValueFunctionWrapsPrecomputedValues.

@SeededTest
void offsetValueFunctionWrapsPrecomputedValues(RandomSeed seed) {
    final int n = 3;
    final UniformRandomProvider r = RngUtils.create(seed.getSeed());
    final ValueFunction f0 = new FakeGradientFunction(3, n);
    final int size = f0.size();
    final double[] b1 = GdscSmlmTestUtils.generateDoubles(size, r);
    final double[] b2 = GdscSmlmTestUtils.generateDoubles(size, r);
    final ValueFunction f1 = OffsetValueFunction.wrapValueFunction(f0, b1);
    final ValueFunction f2 = OffsetValueFunction.wrapValueFunction(f1, b2);
    final double[] p = new double[n];
    for (int i = 0; i < n; i++) {
        p[i] = r.nextDouble();
    }
    final double[] v0 = evaluateValueFunction(f0, p);
    final double[] v1 = evaluateValueFunction(f1, p);
    final double[] v2 = evaluateValueFunction(f2, p);
    for (int i = 0; i < v0.length; i++) {
        final double e = v0[i] + b1[i] + b2[i];
        final double o1 = v1[i] + b2[i];
        final double o2 = v2[i];
        Assertions.assertEquals(e, o1, "o1");
        Assertions.assertEquals(e, o2, 1e-6, "o2");
    }
}

Example 53 with SeededTest

use of uk.ac.sussex.gdsc.test.junit5.SeededTest in project GDSC-SMLM by aherbert.

the class OffsetFunctionTest method offsetGradient2FunctionWrapsPrecomputedValues.

@SeededTest
void offsetGradient2FunctionWrapsPrecomputedValues(RandomSeed seed) {
    final int n = 3;
    final UniformRandomProvider r = RngUtils.create(seed.getSeed());
    final Gradient2Function f0 = new FakeGradientFunction(3, n);
    final int size = f0.size();
    final double[] b1 = GdscSmlmTestUtils.generateDoubles(size, r);
    final double[] b2 = GdscSmlmTestUtils.generateDoubles(size, r);
    final Gradient2Function f1 = OffsetGradient2Function.wrapGradient2Function(f0, b1);
    final Gradient2Function f2 = OffsetGradient2Function.wrapGradient2Function(f1, b2);
    final double[] p = new double[n];
    for (int i = 0; i < n; i++) {
        p[i] = r.nextDouble();
    }
    final double[] d0 = new double[n];
    final double[] d1 = new double[n];
    final double[] d2 = new double[n];
    final double[] d20 = new double[n];
    final double[] d21 = new double[n];
    final double[] d22 = new double[n];
    final double[] v0 = evaluateGradient2Function(f0, p, d0, d20);
    final double[] v1 = evaluateGradient2Function(f1, p, d1, d21);
    final double[] v2 = evaluateGradient2Function(f2, p, d2, d22);
    for (int i = 0; i < v0.length; i++) {
        final double e = v0[i] + b1[i] + b2[i];
        final double o1 = v1[i] + b2[i];
        final double o2 = v2[i];
        Assertions.assertEquals(e, o1, "o1");
        Assertions.assertEquals(e, o2, 1e-6, "o2");
    }
    Assertions.assertArrayEquals(d0, d1, "d1");
    Assertions.assertArrayEquals(d0, d2, "d2");
    Assertions.assertArrayEquals(d20, d21, "d21");
    Assertions.assertArrayEquals(d20, d22, "d22");
}

Example 54 with SeededTest

use of uk.ac.sussex.gdsc.test.junit5.SeededTest in project GDSC-SMLM by aherbert.

the class ScmosLikelihoodWrapperTest method fitEllipticalComputesGradient.

@SeededTest
void fitEllipticalComputesGradient(RandomSeed seed) {
    // The elliptical function gradient evaluation is worse
    final DoubleEquality tmp = eq;
    eq = eqPerDatum;
    functionComputesGradient(seed, GaussianFunctionFactory.FIT_ELLIPTICAL);
    eq = tmp;
}

Example 55 with SeededTest

use of uk.ac.sussex.gdsc.test.junit5.SeededTest in project GDSC-SMLM by aherbert.

the class PrecomputedFunctionTest method precomputedValueFunctionWrapsPrecomputedValues.

@SeededTest
void precomputedValueFunctionWrapsPrecomputedValues(RandomSeed seed) {
    final UniformRandomProvider r = RngUtils.create(seed.getSeed());
    final int size = 100;
    final double[] v = GdscSmlmTestUtils.generateDoubles(size, r);
    final ValueFunction func = new PrecomputedValueFunction(v);
    final double[] vo = evaluateValueFunction(func);
    Assertions.assertArrayEquals(v, vo, "values");
}