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

Example 1 with HoltzerAstigmatismZModel

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

the class CreateData method createPsfModel.

private PsfModel createPsfModel(List<LocalisationModelSet> localisationSets) {
    // Allow reuse of the cached model
    if (psfModelCache != null) {
        return psfModelCache;
    }
    if (psfModelType == PSF_MODEL_IMAGE) {
        return createImagePsf(localisationSets);
    }
    if (psfModelType == PSF_MODEL_ASTIGMATISM) {
        astigmatismModel = AstigmatismModelManager.getModel(settings.getAstigmatismModel());
        if (astigmatismModel == null) {
            throw new IllegalArgumentException("Failed to load model: " + settings.getAstigmatismModel());
        }
        // Convert for simulation
        try {
            if (DoubleEquality.relativeError(astigmatismModel.getNmPerPixel(), settings.getPixelPitch()) > 1e-6) {
                final String message = String.format("Astigmatism model '%s' calibration (%s nm) does not match pixel pitch (%s nm)", settings.getAstigmatismModel(), MathUtils.rounded(astigmatismModel.getNmPerPixel()), MathUtils.rounded(settings.getPixelPitch()));
                // Optionally convert
                final GenericDialog gd = new GenericDialog(TITLE);
                gd.addMessage(TextUtils.wrap(message + ". Created data is not suitable for fitting.", 80));
                gd.addMessage(TextUtils.wrap("Click OK to continue anyway (i.e. draw the spot using the " + "correct nm width on the different sized pixels).", 80));
                gd.showDialog();
                if (gd.wasCanceled()) {
                    throw new IllegalArgumentException(message);
                }
                // Convert to nm
                astigmatismModel = AstigmatismModelManager.convert(astigmatismModel, DistanceUnit.NM, DistanceUnit.NM);
                // Reset pixel pitch. This will draw the spot using the correct size on the different size
                // pixels.
                astigmatismModel = astigmatismModel.toBuilder().setNmPerPixel(settings.getPixelPitch()).build();
            }
            // Convert for simulation in pixels
            astigmatismModel = AstigmatismModelManager.convert(astigmatismModel, DistanceUnit.PIXEL, DistanceUnit.PIXEL);
            return new GaussianPsfModel(AstigmatismModelManager.create(astigmatismModel));
        } catch (final ConversionException ex) {
            // Wrap so this can be caught as the same type
            throw new IllegalArgumentException(ex);
        }
    }
    final double d = settings.getDepthOfFocus() / settings.getPixelPitch();
    if (psfModelType == PSF_MODEL_GAUSSIAN) {
        final double sd = getPsfSd();
        final double gamma = 0;
        final HoltzerAstigmatismZModel zModel = HoltzerAstigmatismZModel.create(sd, sd, gamma, d, 0, 0, 0, 0);
        final GaussianPsfModel m = new GaussianPsfModel(zModel);
        // m.setRange(10);
        return m;
    }
    // Default to Airy pattern
    final double width = getPsfSd() / PsfCalculator.AIRY_TO_GAUSSIAN;
    final AiryPsfModel m = new AiryPsfModel(width, width, d);
    m.setRing(2);
    return m;
}

Example 2 with HoltzerAstigmatismZModel

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

the class FastMleJacobianGradient2ProcedureTest method gradientCalculatorComputesGradient.

@Override
@SeededTest
void gradientCalculatorComputesGradient(RandomSeed seed) {
    gradientCalculatorComputesGradient(seed, 1, new SingleFreeCircularErfGaussian2DFunction(blockWidth, blockWidth));
    gradientCalculatorComputesGradient(seed, 2, new MultiFreeCircularErfGaussian2DFunction(2, blockWidth, blockWidth));
    // Use a reasonable z-depth function from the Smith, et al (2010) paper (page 377)
    final double sx = 1.08;
    final double sy = 1.01;
    final double gamma = 0.389;
    final double d = 0.531;
    final double Ax = -0.0708;
    final double Bx = -0.073;
    final double Ay = 0.164;
    final double By = 0.0417;
    final HoltzerAstigmatismZModel zModel = HoltzerAstigmatismZModel.create(sx, sy, gamma, d, Ax, Bx, Ay, By);
    gradientCalculatorComputesGradient(seed, 1, new SingleAstigmatismErfGaussian2DFunction(blockWidth, blockWidth, zModel));
}

Example 3 with HoltzerAstigmatismZModel

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

the class FastMleGradient2ProcedureTest method gradientCalculatorComputesGradient.

@SeededTest
void gradientCalculatorComputesGradient(RandomSeed seed) {
    gradientCalculatorComputesGradient(seed, new SingleFreeCircularErfGaussian2DFunction(blockWidth, blockWidth));
    // Use a reasonable z-depth function from the Smith, et al (2010) paper (page 377)
    final double sx = 1.08;
    final double sy = 1.01;
    final double gamma = 0.389;
    final double d = 0.531;
    final double Ax = -0.0708;
    final double Bx = -0.073;
    final double Ay = 0.164;
    final double By = 0.0417;
    final HoltzerAstigmatismZModel zModel = HoltzerAstigmatismZModel.create(sx, sy, gamma, d, Ax, Bx, Ay, By);
    gradientCalculatorComputesGradient(seed, new SingleAstigmatismErfGaussian2DFunction(blockWidth, blockWidth, zModel));
}

Example 4 with HoltzerAstigmatismZModel

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

the class AstigmatismModelManager method viewModel.

private void viewModel() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    final String[] models = listAstigmatismModels(false);
    gd.addChoice("Model", models, pluginSettings.getSelected());
    gd.addChoice("z_distance_unit", SettingsManager.getDistanceUnitNames(), pluginSettings.getZDistanceUnitValue());
    gd.addChoice("s_distance_unit", SettingsManager.getDistanceUnitNames(), pluginSettings.getSDistanceUnitValue());
    gd.addCheckbox("Show_depth_of_focus", pluginSettings.getShowDepthOfFocus());
    gd.addCheckbox("Show_combined_width", pluginSettings.getShowCombinedWidth());
    gd.addCheckbox("Show_PSF", pluginSettings.getShowPsf());
    gd.addHelp(HelpUrls.getUrl("astigmatism-model-manager-view"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    final String name = gd.getNextChoice();
    pluginSettings.setSelected(name);
    pluginSettings.setZDistanceUnitValue(gd.getNextChoiceIndex());
    pluginSettings.setSDistanceUnitValue(gd.getNextChoiceIndex());
    pluginSettings.setShowDepthOfFocus(gd.getNextBoolean());
    pluginSettings.setShowCombinedWidth(gd.getNextBoolean());
    pluginSettings.setShowPsf(gd.getNextBoolean());
    // Try and get the named resource
    AstigmatismModel model = AstigmatismModelSettingsHolder.getSettings().getAstigmatismModelResourcesMap().get(name);
    if (model == null) {
        IJ.error(TITLE, "Failed to find astigmatism model: " + name);
        return;
    }
    try {
        model = convert(model, pluginSettings.getZDistanceUnit(), pluginSettings.getSDistanceUnit());
    } catch (final ConversionException ex) {
        ImageJUtils.log("Bad conversion (%s), defaulting to native model units", ex.getMessage());
    }
    ImageJUtils.log("Astigmatism model: %s\n%s", name, model);
    // Plot the curve. Do this so we encompass twice the depth-of-field.
    final double gamma = model.getGamma();
    final double d = model.getD();
    final double s0x = model.getS0X();
    final double Ax = model.getAx();
    final double Bx = model.getBx();
    final double s0y = model.getS0Y();
    final double Ay = model.getAy();
    final double By = model.getBy();
    final double range = Math.abs(gamma) + 1.5 * d;
    final int n = 200;
    final double step = range / n;
    final double[] z = new double[2 * n + 1];
    final double[] sx = new double[z.length];
    final double[] sy = new double[z.length];
    // Use the same class that is used during fitting
    final HoltzerAstigmatismZModel m = HoltzerAstigmatismZModel.create(s0x, s0y, gamma, d, Ax, Bx, Ay, By);
    for (int i = 0; i < z.length; i++) {
        final double zz = -range + i * step;
        z[i] = zz;
        sx[i] = m.getSx(zz);
        sy[i] = m.getSy(zz);
    }
    final String title = TITLE + " Width Curve";
    final Plot plot = new Plot(title, "Z (" + UnitHelper.getShortName(model.getZDistanceUnit()) + ")", "Width (" + UnitHelper.getShortName(model.getSDistanceUnit()) + ")");
    double[] limits = MathUtils.limits(sx);
    limits = MathUtils.limits(limits, sy);
    final double rangex = (z[z.length - 1] - z[0]) * 0.05;
    final double rangey = (limits[1] - limits[0]) * 0.05;
    final double miny = limits[0] - rangey;
    final double maxy = limits[1] + rangey;
    plot.setLimits(z[0] - rangex, z[z.length - 1] + rangex, miny, maxy);
    plot.setColor(Color.RED);
    plot.addPoints(z, sx, Plot.LINE);
    plot.setColor(Color.BLUE);
    plot.addPoints(z, sy, Plot.LINE);
    plot.setColor(Color.YELLOW);
    if (pluginSettings.getShowDepthOfFocus()) {
        final double z0x = gamma;
        final double z0y = -gamma;
        plot.setColor(Color.RED.darker());
        plot.drawDottedLine(z0x - d, miny, z0x - d, maxy, 4);
        plot.drawDottedLine(z0x + d, miny, z0x + d, maxy, 4);
        plot.setColor(Color.BLUE.darker());
        plot.drawDottedLine(z0y - d, miny, z0y - d, maxy, 4);
        plot.drawDottedLine(z0y + d, miny, z0y + d, maxy, 4);
    }
    String legend = "Sx\nSy";
    if (pluginSettings.getShowCombinedWidth()) {
        final double[] s = new double[z.length];
        for (int i = 0; i < z.length; i++) {
            s[i] = Gaussian2DPeakResultHelper.getStandardDeviation(sx[i], sy[i]);
        }
        plot.setColor(Color.GREEN);
        plot.addPoints(z, s, Plot.LINE);
        legend += "\tS";
    }
    plot.setColor(Color.BLACK);
    plot.addLegend(legend);
    plot.addLabel(0, 0, String.format("Model = %s (%s nm/pixel)", name, MathUtils.rounded(model.getNmPerPixel())));
    ImageJUtils.display(title, plot);
    if (!pluginSettings.getShowPsf()) {
        return;
    }
    // Get pixel range using 3x[max SD]
    final int width = 1 + 2 * ((int) Math.ceil(limits[1] * 3));
    new ModelRenderer(name, model, m, range, width, plot).run();
}