Examples with Type gdsc.smlm.fitting.nonlinear.gradient.LVMGradientProcedureFactory.Type used on opensource projects

Example 1 with Type

use of gdsc.smlm.fitting.nonlinear.gradient.LVMGradientProcedureFactory.Type in project GDSC-SMLM by aherbert.

the class LVMGradientProcedureTest method gradientProcedureIsNotSlowerThanGradientCalculator.

private void gradientProcedureIsNotSlowerThanGradientCalculator(final int nparams, final boolean mle) {
    org.junit.Assume.assumeTrue(speedTests || TestSettings.RUN_SPEED_TESTS);
    final int iter = 1000;
    rdg = new RandomDataGenerator(new Well19937c(30051977));
    final double[][] alpha = new double[nparams][nparams];
    final double[] beta = new double[nparams];
    final ArrayList<double[]> paramsList = new ArrayList<double[]>(iter);
    final ArrayList<double[]> yList = new ArrayList<double[]>(iter);
    int[] x = createFakeData(nparams, iter, paramsList, yList);
    final int n = x.length;
    final FakeGradientFunction func = new FakeGradientFunction(blockWidth, nparams);
    GradientCalculator calc = GradientCalculatorFactory.newCalculator(nparams, mle);
    for (int i = 0; i < paramsList.size(); i++) calc.findLinearised(n, yList.get(i), paramsList.get(i), alpha, beta, func);
    final Type type = (mle) ? Type.MLE : Type.LSQ;
    for (int i = 0; i < paramsList.size(); i++) {
        LVMGradientProcedure p = LVMGradientProcedureFactory.create(yList.get(i), func, type);
        p.gradient(paramsList.get(i));
    }
    // Realistic loops for an optimisation
    final int loops = 15;
    // Run till stable timing
    Timer t1 = new Timer() {

        @Override
        void run() {
            for (int i = 0, k = 0; i < iter; i++) {
                GradientCalculator calc = GradientCalculatorFactory.newCalculator(nparams, mle);
                for (int j = loops; j-- > 0; ) calc.findLinearised(n, yList.get(i), paramsList.get(k++ % iter), alpha, beta, func);
            }
        }
    };
    long time1 = t1.getTime();
    Timer t2 = new Timer(t1.loops) {

        @Override
        void run() {
            for (int i = 0, k = 0; i < iter; i++) {
                LVMGradientProcedure p = LVMGradientProcedureFactory.create(yList.get(i), func, type);
                for (int j = loops; j-- > 0; ) p.gradient(paramsList.get(k++ % iter));
            }
        }
    };
    long time2 = t2.getTime();
    log("GradientCalculator = %d : LVMGradientProcedure %d %b = %d : %fx\n", time1, nparams, mle, time2, (1.0 * time1) / time2);
    if (TestSettings.ASSERT_SPEED_TESTS) {
        // Add contingency
        Assert.assertTrue(time2 < time1 * 1.5);
    }
}