Examples with FakeGradientFunction uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction used on opensource projects

Example 6 with FakeGradientFunction

use of uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction in project GDSC-SMLM by aherbert.

the class ParameterBoundsTest method canDoubleBoundParameter.

@Test
void canDoubleBoundParameter() {
    final ParameterBounds bounds = new ParameterBounds(new FakeGradientFunction(1, 1, 1));
    final double s = 2;
    bounds.setBounds(new double[] { -s }, new double[] { s });
    final double[] a1 = new double[1];
    final double[] a2 = new double[1];
    bounds.applyBounds(a1, new double[] { 10 }, a2);
    Assertions.assertArrayEquals(a2, new double[] { s }, "Step 10");
    bounds.applyBounds(a1, new double[] { -10 }, a2);
    Assertions.assertArrayEquals(a2, new double[] { -s }, "Step -10");
}

Example 7 with FakeGradientFunction

use of uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction in project GDSC-SMLM by aherbert.

the class WPoissonGradientProcedureTest method gradientProcedureUnrolledComputesSameAsGradientProcedure.

private void gradientProcedureUnrolledComputesSameAsGradientProcedure(RandomSeed seed, int nparams, boolean precomputed) {
    final int iter = 10;
    final ArrayList<double[]> paramsList = new ArrayList<>(iter);
    final UniformRandomProvider rng = RngUtils.create(seed.getSeed());
    createFakeParams(rng, nparams, iter, paramsList);
    final Gradient1Function func = new FakeGradientFunction(blockWidth, nparams);
    final double[] v = (precomputed) ? dataCache.computeIfAbsent(seed, WPoissonGradientProcedureTest::createData) : null;
    final IntArrayFormatSupplier msg = getMessage(nparams, "[%d] Observations: Not same linear @ %d");
    for (int i = 0; i < paramsList.size(); i++) {
        final double[] y = createFakeData(rng);
        final WPoissonGradientProcedure p1 = new WPoissonGradientProcedure(y, v, func);
        p1.computeFisherInformation(paramsList.get(i));
        final WPoissonGradientProcedure p2 = WPoissonGradientProcedureUtils.create(y, v, func);
        p2.computeFisherInformation(paramsList.get(i));
        // Exactly the same ...
        Assertions.assertArrayEquals(p1.getLinear(), p2.getLinear(), msg.set(1, i));
    }
}

Example 8 with FakeGradientFunction

use of uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction in project GDSC-SMLM by aherbert.

the class WPoissonGradientProcedureTest method gradientProcedureIsFasterThanWLseGradientProcedure.

private void gradientProcedureIsFasterThanWLseGradientProcedure(RandomSeed seed, final int nparams) {
    Assumptions.assumeTrue(TestSettings.allow(TestComplexity.MEDIUM));
    final int iter = 100;
    final ArrayList<double[]> paramsList = new ArrayList<>(iter);
    final ArrayList<double[]> yList = new ArrayList<>(iter);
    final double[] var = dataCache.computeIfAbsent(seed, WPoissonGradientProcedureTest::createData);
    createFakeData(RngUtils.create(seed.getSeed()), nparams, iter, paramsList, yList);
    // Remove the timing of the function call by creating a dummy function
    final FakeGradientFunction func = new FakeGradientFunction(blockWidth, nparams);
    final IntArrayFormatSupplier msg = new IntArrayFormatSupplier("M [%d]", 1);
    for (int i = 0; i < paramsList.size(); i++) {
        final double[] y = yList.get(i);
        final WLsqLvmGradientProcedure p1 = WLsqLvmGradientProcedureUtils.create(y, var, func);
        p1.gradient(paramsList.get(i));
        final WPoissonGradientProcedure p2 = WPoissonGradientProcedureUtils.create(y, var, func);
        p2.computeFisherInformation(paramsList.get(i));
        // Check they are the same
        Assertions.assertArrayEquals(p1.getAlphaLinear(), p2.getLinear(), msg.set(0, i));
    }
    // Realistic loops for an optimisation
    final int loops = 15;
    // Run till stable timing
    final Timer t1 = new Timer() {

        @Override
        void run() {
            for (int i = 0, k = 0; i < paramsList.size(); i++) {
                final WLsqLvmGradientProcedure p1 = WLsqLvmGradientProcedureUtils.create(yList.get(i), var, func);
                for (int j = loops; j-- > 0; ) {
                    p1.gradient(paramsList.get(k++ % iter));
                }
            }
        }
    };
    final long time1 = t1.getTime();
    final Timer t2 = new Timer(t1.loops) {

        @Override
        void run() {
            for (int i = 0, k = 0; i < paramsList.size(); i++) {
                final WPoissonGradientProcedure p2 = WPoissonGradientProcedureUtils.create(yList.get(i), var, func);
                for (int j = loops; j-- > 0; ) {
                    p2.computeFisherInformation(paramsList.get(k++ % iter));
                }
            }
        }
    };
    final long time2 = t2.getTime();
    logger.log(TestLogUtils.getTimingRecord("WLsqLvmGradientProcedure " + nparams, time1, "WPoissonGradientProcedure", time2));
}

Example 9 with FakeGradientFunction

use of uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction in project GDSC-SMLM by aherbert.

the class LsqVarianceGradientProcedureTest method gradientProcedureIsFasterUnrolledThanGradientProcedure.

private void gradientProcedureIsFasterUnrolledThanGradientProcedure(RandomSeed seed, final int nparams, final boolean precomputed) {
    Assumptions.assumeTrue(TestSettings.allow(TestComplexity.MEDIUM));
    final int iter = 100;
    final ArrayList<double[]> paramsList = new ArrayList<>(iter);
    createFakeParams(RngUtils.create(seed.getSeed()), nparams, iter, paramsList);
    // Remove the timing of the function call by creating a dummy function
    final FakeGradientFunction f = new FakeGradientFunction(blockWidth, nparams);
    final Gradient1Function func = (precomputed) ? OffsetGradient1Function.wrapGradient1Function(f, SimpleArrayUtils.newArray(f.size(), 0.1, 1.3)) : f;
    final IndexSupplier msg = new IndexSupplier(1, "M ", null);
    for (int i = 0; i < paramsList.size(); i++) {
        final LsqVarianceGradientProcedure p1 = new LsqVarianceGradientProcedure(func);
        p1.variance(paramsList.get(i));
        p1.variance(paramsList.get(i));
        final LsqVarianceGradientProcedure p2 = LsqVarianceGradientProcedureUtils.create(func);
        p2.variance(paramsList.get(i));
        p2.variance(paramsList.get(i));
        // Check they are the same
        Assertions.assertArrayEquals(p1.variance, p2.variance, msg.set(0, i));
    }
    // Realistic loops for an optimisation
    final int loops = 15;
    // Run till stable timing
    final Timer t1 = new Timer() {

        @Override
        void run() {
            for (int i = 0, k = 0; i < paramsList.size(); i++) {
                final LsqVarianceGradientProcedure p1 = new LsqVarianceGradientProcedure(func);
                for (int j = loops; j-- > 0; ) {
                    p1.variance(paramsList.get(k++ % iter));
                }
            }
        }
    };
    final long time1 = t1.getTime();
    final Timer t2 = new Timer(t1.loops) {

        @Override
        void run() {
            for (int i = 0, k = 0; i < paramsList.size(); i++) {
                final LsqVarianceGradientProcedure p2 = LsqVarianceGradientProcedureUtils.create(func);
                for (int j = loops; j-- > 0; ) {
                    p2.variance(paramsList.get(k++ % iter));
                }
            }
        }
    };
    final long time2 = t2.getTime();
    logger.log(TestLogUtils.getTimingRecord("precomputed=" + precomputed + " Standard " + nparams, time1, "Unrolled", time2));
}

Example 10 with FakeGradientFunction

use of uk.ac.sussex.gdsc.smlm.function.FakeGradientFunction in project GDSC-SMLM by aherbert.

the class LsqVarianceGradientProcedureTest method gradientProcedureUnrolledComputesSameAsGradientProcedure.

private void gradientProcedureUnrolledComputesSameAsGradientProcedure(RandomSeed seed, int nparams, boolean precomputed) {
    final int iter = 10;
    final ArrayList<double[]> paramsList = new ArrayList<>(iter);
    createFakeParams(RngUtils.create(seed.getSeed()), nparams, iter, paramsList);
    Gradient1Function func = new FakeGradientFunction(blockWidth, nparams);
    if (precomputed) {
        func = OffsetGradient1Function.wrapGradient1Function(func, SimpleArrayUtils.newArray(func.size(), 0.1, 1.3));
    }
    final IntArrayFormatSupplier msg = new IntArrayFormatSupplier("[%d] Observations: Not same variance @ %d", 2);
    msg.set(0, nparams);
    for (int i = 0; i < paramsList.size(); i++) {
        final LsqVarianceGradientProcedure p1 = new LsqVarianceGradientProcedure(func);
        p1.variance(paramsList.get(i));
        final LsqVarianceGradientProcedure p2 = LsqVarianceGradientProcedureUtils.create(func);
        p2.variance(paramsList.get(i));
        // Exactly the same ...
        Assertions.assertArrayEquals(p1.variance, p2.variance, msg.set(1, i));
    }
}