Examples with Gaussian2DFunction gdsc.smlm.function.gaussian.Gaussian2DFunction used on opensource projects

Example 21 with Gaussian2DFunction

use of gdsc.smlm.function.gaussian.Gaussian2DFunction in project GDSC-SMLM by aherbert.

the class PoissonLikelihoodWrapperTest method functionComputesGradient.

private void functionComputesGradient(int flags) {
    Gaussian2DFunction f1 = GaussianFunctionFactory.create2D(1, maxx, maxx, flags, null);
    // Setup
    testbackground = testbackground_;
    testamplitude1 = testamplitude1_;
    testangle1 = testangle1_;
    testcx1 = testcx1_;
    testcy1 = testcy1_;
    testw1 = testw1_;
    if (!f1.evaluatesBackground()) {
        testbackground = new double[] { testbackground[0] };
    }
    if (!f1.evaluatesSignal()) {
        testamplitude1 = new double[] { testamplitude1[0] };
    }
    if (!f1.evaluatesShape()) {
        testangle1 = new double[] { 0 };
    }
    // Position is always evaluated
    boolean noSecondWidth = false;
    if (!f1.evaluatesSD0()) {
        // Just use 1 width
        testw1 = new double[][] { testw1[0] };
        // If no width 0 then assume we have no width 1 as well
        noSecondWidth = true;
    } else if (!f1.evaluatesSD1()) {
        // No evaluation of second width needs only variation in width 0 so truncate 
        testw1 = Arrays.copyOf(testw1, 2);
        noSecondWidth = true;
    }
    if (noSecondWidth) {
        for (int i = 0; i < testw1.length; i++) {
            testw1[i][1] = testw1[i][0];
        }
    }
    double fraction = 90;
    if (f1.evaluatesBackground())
        functionComputesTargetGradient(f1, Gaussian2DFunction.BACKGROUND, fraction);
    if (f1.evaluatesSignal())
        functionComputesTargetGradient(f1, Gaussian2DFunction.SIGNAL, fraction);
    if (f1.evaluatesShape())
        functionComputesTargetGradient(f1, Gaussian2DFunction.SHAPE, fraction);
    functionComputesTargetGradient(f1, Gaussian2DFunction.X_POSITION, fraction);
    functionComputesTargetGradient(f1, Gaussian2DFunction.Y_POSITION, fraction);
    if (f1.evaluatesSD0())
        functionComputesTargetGradient(f1, Gaussian2DFunction.X_SD, fraction);
    if (f1.evaluatesSD1())
        functionComputesTargetGradient(f1, Gaussian2DFunction.Y_SD, fraction);
}

Example 22 with Gaussian2DFunction

use of gdsc.smlm.function.gaussian.Gaussian2DFunction in project GDSC-SMLM by aherbert.

the class SpeedTest method f1FasterThanf2.

void f1FasterThanf2(int npeaks, int flags1, int flags2) {
    org.junit.Assume.assumeTrue(TestSettings.RUN_SPEED_TESTS);
    ArrayList<double[]> paramsList2 = (npeaks == 1) ? paramsListSinglePeak : paramsListDoublePeak;
    // Use the full list of parameters to build the functions
    Gaussian2DFunction f1 = GaussianFunctionFactory.create2D(npeaks, blockWidth, blockWidth, flags1, null);
    Gaussian2DFunction f2 = GaussianFunctionFactory.create2D(npeaks, blockWidth, blockWidth, flags2, null);
    double[] dyda = new double[1 + npeaks * 6];
    for (int i = 0; i < paramsList2.size(); i++) {
        f1.initialise(paramsList2.get(i));
        for (int j = 0; j < x.length; j++) f1.eval(x[j], dyda);
    }
    long start1 = System.nanoTime();
    for (int i = 0; i < paramsList2.size(); i++) {
        f1.initialise(paramsList2.get(i));
        for (int j = 0; j < x.length; j++) f1.eval(x[j], dyda);
    }
    start1 = System.nanoTime() - start1;
    for (int i = 0; i < paramsList2.size(); i++) {
        f2.initialise(paramsList2.get(i));
        for (int j = 0; j < x.length; j++) f2.eval(x[j], dyda);
    }
    long start2 = System.nanoTime();
    for (int i = 0; i < paramsList2.size(); i++) {
        f2.initialise(paramsList2.get(i));
        for (int j = 0; j < x.length; j++) f2.eval(x[j], dyda);
    }
    start2 = System.nanoTime() - start2;
    log("%s = %d : %s = %d : %fx\n", f1.getClass().getName(), start1, f2.getClass().getName(), start2, (1.0 * start2) / start1);
    if (TestSettings.ASSERT_SPEED_TESTS)
        Assert.assertTrue(start2 > start1);
}

Example 23 with Gaussian2DFunction

use of gdsc.smlm.function.gaussian.Gaussian2DFunction in project GDSC-SMLM by aherbert.

the class Gaussian2DFunctionTest method functionComputesTargetWithAndWithoutGradientWith2Peaks.

@Test
public void functionComputesTargetWithAndWithoutGradientWith2Peaks() {
    if (f2 == null)
        return;
    double[] dyda = new double[f2.gradientIndices().length];
    double[] a;
    boolean record = true;
    for (double background : testbackground) // Peak 1
    for (double amplitude1 : testamplitude1) for (double shape1 : testshape1) for (double cx1 : testcx1) for (double cy1 : testcy1) for (double[] w1 : testw1) // Peak 2
    for (double amplitude2 : testamplitude2) for (double shape2 : testshape2) for (double cx2 : testcx2) for (double cy2 : testcy2) for (double[] w2 : testw2) {
        a = createParameters(background, amplitude1, shape1, cx1, cy1, w1[0], w1[1], amplitude2, shape2, cx2, cy2, w2[0], w2[1]);
        f2.initialise(a);
        // Test the frozen version
        int flags = GaussianFunctionFactory.freeze(2, this.flags, zModel, a);
        Gaussian2DFunction f = GaussianFunctionFactory.create2D(2, f2.getMaxX(), f2.getMaxY(), flags, zModel);
        f.initialise(a);
        if (record) {
            record = false;
            log("%s %d frozen to %s\n", f2.getClass().getSimpleName(), 2, f.getClass().getSimpleName());
        }
        for (int x : testx) for (int y : testy) {
            int xx = y * maxx + x;
            double y1 = f2.eval(xx, dyda);
            double y2 = f2.eval(xx);
            Assert.assertTrue(y1 + " != " + y2, eq2.almostEqualRelativeOrAbsolute(y1, y2));
            y2 = f.eval(xx);
            Assert.assertTrue(y1 + " != frozen " + y2, eq2.almostEqualRelativeOrAbsolute(y1, y2));
        }
    }
}

Example 24 with Gaussian2DFunction

use of gdsc.smlm.function.gaussian.Gaussian2DFunction in project GDSC-SMLM by aherbert.

the class Gaussian2DFunctionTest method functionComputesTargetGradientWith2Peaks.

private void functionComputesTargetGradientWith2Peaks(int targetParameter) {
    int gradientIndex = findGradientIndex(f2, targetParameter);
    double[] dyda = new double[f2.gradientIndices().length];
    double[] dyda2 = new double[dyda.length];
    double[] a;
    Gaussian2DFunction f2a = GaussianFunctionFactory.create2D(2, maxx, maxy, flags, zModel);
    Gaussian2DFunction f2b = GaussianFunctionFactory.create2D(2, maxx, maxy, flags, zModel);
    Statistics s = new Statistics();
    for (double background : testbackground) // Peak 1
    for (double amplitude1 : testamplitude1) for (double shape1 : testshape1) for (double cx1 : testcx1) for (double cy1 : testcy1) for (double[] w1 : testw1) // Peak 2
    for (double amplitude2 : testamplitude2) for (double shape2 : testshape2) for (double cx2 : testcx2) for (double cy2 : testcy2) for (double[] w2 : testw2) {
        a = createParameters(background, amplitude1, shape1, cx1, cy1, w1[0], w1[1], amplitude2, shape2, cx2, cy2, w2[0], w2[1]);
        f2.initialise(a);
        // Numerically solve gradient. 
        // Calculate the step size h to be an exact numerical representation
        final double xx = a[targetParameter];
        // Get h to minimise roundoff error
        double h = Precision.representableDelta(xx, h_);
        // Evaluate at (x+h) and (x-h)
        a = createParameters(background, amplitude1, shape1, cx1, cy1, w1[0], w1[1], amplitude2, shape2, cx2, cy2, w2[0], w2[1]);
        a[targetParameter] = xx + h;
        f2a.initialise(a);
        a = createParameters(background, amplitude1, shape1, cx1, cy1, w1[0], w1[1], amplitude2, shape2, cx2, cy2, w2[0], w2[1]);
        a[targetParameter] = xx - h;
        f2b.initialise(a);
        for (int x : testx) for (int y : testy) {
            int i = y * maxx + x;
            f2.eval(i, dyda);
            double value2 = f2a.eval(i, dyda2);
            double value3 = f2b.eval(i, dyda2);
            double gradient = (value2 - value3) / (2 * h);
            double error = DoubleEquality.relativeError(gradient, dyda2[gradientIndex]);
            s.add(error);
            Assert.assertTrue(gradient + " sign != " + dyda2[gradientIndex], (gradient * dyda2[gradientIndex]) >= 0);
            //System.out.printf("[%d,%d] %f == [%d] %f? (%g)\n", x, y, gradient,
            //		gradientIndex, dyda2[gradientIndex], error);
            //System.out.printf("[%d,%d] %f == [%d] %f?\n", x, y, gradient, gradientIndex, dyda[gradientIndex]);
            Assert.assertTrue(gradient + " != " + dyda[gradientIndex], eq.almostEqualRelativeOrAbsolute(gradient, dyda[gradientIndex]));
        }
    }
    System.out.printf("functionComputesTargetGradientWith2Peaks %s [%d] %s (error %s +/- %s)\n", f2.getClass().getSimpleName(), Gaussian2DFunction.getPeak(targetParameter), f2.getName(targetParameter), Utils.rounded(s.getMean()), Utils.rounded(s.getStandardDeviation()));
}

Example 25 with Gaussian2DFunction

use of gdsc.smlm.function.gaussian.Gaussian2DFunction in project GDSC-SMLM by aherbert.

the class Gaussian2DFunctionTest method factoryCreatesCorrectFunction.

@Test
public void factoryCreatesCorrectFunction() {
    Gaussian2DFunction f;
    if (f2 != null) {
        f = GaussianFunctionFactory.create2D(2, maxx, maxy, flags, zModel);
        Assert.assertTrue("Incorrect function2", f.getClass() == f2.getClass());
    } else {
        f = GaussianFunctionFactory.create2D(1, maxx, maxy, flags, zModel);
        Assert.assertTrue("Incorrect function1", f.getClass() == f1.getClass());
    }
}