Examples with LutLoader ij.plugin.LutLoader used on opensource projects

Example 1 with LutLoader

use of ij.plugin.LutLoader in project GDSC-SMLM by aherbert.

the class DiffusionRateTest method showExample.

private void showExample(int totalSteps, double diffusionSigma, UniformRandomProvider rng) {
    final MoleculeModel m = new MoleculeModel(0, new double[3]);
    final float[] xValues = new float[totalSteps];
    final float[] x = new float[totalSteps];
    final float[] y = new float[totalSteps];
    final DiffusionType diffusionType = CreateDataSettingsHelper.getDiffusionType(settings.getDiffusionType());
    double[] axis;
    if (diffusionType == DiffusionType.LINEAR_WALK) {
        axis = nextVector(SamplerUtils.createNormalizedGaussianSampler(rng));
    } else {
        axis = null;
    }
    for (int j = 0; j < totalSteps; j++) {
        if (diffusionType == DiffusionType.GRID_WALK) {
            m.walk(diffusionSigma, rng);
        } else if (diffusionType == DiffusionType.LINEAR_WALK) {
            m.slide(diffusionSigma, axis, rng);
        } else {
            m.move(diffusionSigma, rng);
        }
        x[j] = (float) (m.getX());
        y[j] = (float) (m.getY());
        xValues[j] = (float) ((j + 1) / settings.getStepsPerSecond());
    }
    // Plot x and y coords on a timeline
    final String title = TITLE + " example coordinates";
    final Plot plot = new Plot(title, "Time (seconds)", "Distance (um)");
    final float[] xUm = convertToUm(x);
    final float[] yUm = convertToUm(y);
    float[] limits = MathUtils.limits(xUm);
    limits = MathUtils.limits(limits, yUm);
    plot.setLimits(0, totalSteps / settings.getStepsPerSecond(), limits[0], limits[1]);
    plot.setColor(Color.red);
    plot.addPoints(xValues, xUm, Plot.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(xValues, yUm, Plot.LINE);
    ImageJUtils.display(title, plot);
    // Scale up and draw 2D position
    for (int j = 0; j < totalSteps; j++) {
        x[j] *= pluginSettings.magnification;
        y[j] *= pluginSettings.magnification;
    }
    final float[] limitsx = getLimits(x);
    final float[] limitsy = getLimits(y);
    int width = (int) (limitsx[1] - limitsx[0]);
    int height = (int) (limitsy[1] - limitsy[0]);
    // Ensure we draw something, even it is a simple dot at the centre for no diffusion
    if (width == 0) {
        width = (int) (32 * pluginSettings.magnification);
        limitsx[0] = -width / 2.0f;
    }
    if (height == 0) {
        height = (int) (32 * pluginSettings.magnification);
        limitsy[0] = -height / 2.0f;
    }
    final ImageProcessor ip = new ByteProcessor(width, height);
    // Adjust x and y using the minimum to centre
    x[0] -= limitsx[0];
    y[0] -= limitsy[0];
    for (int j = 1; j < totalSteps; j++) {
        // Adjust x and y using the minimum to centre
        x[j] -= limitsx[0];
        y[j] -= limitsy[0];
        // Draw a line
        ip.setColor(32 + (223 * j) / (totalSteps - 1));
        ip.drawLine(round(x[j - 1]), round(y[j - 1]), round(x[j]), round(y[j]));
    }
    // Draw the final position
    ip.putPixel(round(x[totalSteps - 1]), round(y[totalSteps - 1]), 255);
    final ImagePlus imp = ImageJUtils.display(TITLE + " example", ip);
    // Apply the fire lookup table
    WindowManager.setTempCurrentImage(imp);
    final LutLoader lut = new LutLoader();
    lut.run("fire");
    WindowManager.setTempCurrentImage(null);
}

Example 2 with LutLoader

use of ij.plugin.LutLoader in project GDSC-SMLM by aherbert.

the class IJImagePeakResults method begin.

/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.utils.fitting.PeakResults#begin()
	 */
public void begin() {
    imageActive = false;
    preBegin();
    // Handle invalid bounds with an empty single pixel image
    boolean validBounds = imageWidth > 0 && imageHeight > 0 && (double) imageWidth * (double) imageHeight < Integer.MAX_VALUE;
    int w, h;
    if (validBounds) {
        w = imageWidth;
        h = imageHeight;
    } else {
        Utils.log("ERROR: Unable to create image results '%s' due to invalid dimensions: width=%d, height=%d", title, imageWidth, imageHeight);
        w = h = 1;
    }
    size = 0;
    lastPaintSize = 0;
    // Let some results appear before drawing
    nextRepaintSize = 20;
    nextPaintTime = System.currentTimeMillis() + repaintDelay;
    imageLock = false;
    data = new double[w * h];
    // Use negative zero so that we know when positive zero has been written to the array.
    if ((displayFlags & (DISPLAY_MAPPED | DISPLAY_MAP_ZERO)) == (DISPLAY_MAPPED | DISPLAY_MAP_ZERO))
        EMPTY = -0.0f;
    resetData();
    imp = WindowManager.getImage(title);
    currentFrame = 1;
    ImageProcessor ip = createNewProcessor(w, h);
    if (imp == null) {
        imp = new ImagePlus(title, ip);
        // Apply the fire lookup table
        WindowManager.setTempCurrentImage(imp);
        LutLoader lut = new LutLoader();
        lut.run(lutName);
        WindowManager.setTempCurrentImage(null);
        if (displayImage)
            imp.show();
    } else {
        // Copy the lookup table
        ip.setColorModel(imp.getProcessor().getColorModel());
        ImageStack stack = createNewImageStack(w, h);
        stack.addSlice(null, ip);
        // If resizing then remove adornments
        if (stack.getWidth() != imp.getWidth() || stack.getHeight() != imp.getHeight()) {
            imp.setOverlay(null);
            imp.setRoi((Roi) null);
        }
        imp.setStack(stack);
        if (displayImage)
            imp.show();
        else
            imp.hide();
    }
    imp.setProperty("Info", createInfo());
    if (calibration != null) {
        Calibration cal = new Calibration();
        String unit = "nm";
        double unitPerPixel = calibration.getNmPerPixel() / scale;
        if (unitPerPixel > 100) {
            unit = "um";
            unitPerPixel /= 1000.0;
        }
        cal.setUnit(unit);
        cal.pixelHeight = cal.pixelWidth = unitPerPixel;
        imp.setCalibration(cal);
    }
    // We cannot draw anything with no bounds
    imageActive = validBounds;
}

Example 3 with LutLoader

use of ij.plugin.LutLoader in project GDSC-SMLM by aherbert.

the class DiffusionRateTest method showExample.

private void showExample(int totalSteps, double diffusionSigma, RandomGenerator[] random) {
    MoleculeModel m = new MoleculeModel(0, new double[3]);
    float[] xValues = new float[totalSteps];
    float[] x = new float[totalSteps];
    float[] y = new float[totalSteps];
    final double[] axis = (settings.getDiffusionType() == DiffusionType.LINEAR_WALK) ? nextVector() : null;
    for (int j = 0; j < totalSteps; j++) {
        if (settings.getDiffusionType() == DiffusionType.GRID_WALK)
            m.walk(diffusionSigma, random);
        else if (settings.getDiffusionType() == DiffusionType.LINEAR_WALK)
            m.slide(diffusionSigma, axis, random[0]);
        else
            m.move(diffusionSigma, random);
        x[j] = (float) (m.getX());
        y[j] = (float) (m.getY());
        xValues[j] = (float) ((j + 1) / settings.stepsPerSecond);
    }
    // Plot x and y coords on a timeline
    String title = TITLE + " example coordinates";
    Plot2 plot = new Plot2(title, "Time (seconds)", "Distance (um)");
    float[] xUm = convertToUm(x);
    float[] yUm = convertToUm(y);
    float[] limits = Maths.limits(xUm);
    limits = Maths.limits(limits, yUm);
    plot.setLimits(0, totalSteps / settings.stepsPerSecond, limits[0], limits[1]);
    plot.setColor(Color.red);
    plot.addPoints(xValues, xUm, Plot2.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(xValues, yUm, Plot2.LINE);
    Utils.display(title, plot);
    // Scale up and draw 2D position
    for (int j = 0; j < totalSteps; j++) {
        x[j] *= magnification;
        y[j] *= magnification;
    }
    float[] limitsx = getLimits(x);
    float[] limitsy = getLimits(y);
    int width = (int) (limitsx[1] - limitsx[0]);
    int height = (int) (limitsy[1] - limitsy[0]);
    // Ensure we draw something, even it is a simple dot at the centre for no diffusion
    if (width == 0) {
        width = (int) (32 * magnification);
        limitsx[0] = -width / 2;
    }
    if (height == 0) {
        height = (int) (32 * magnification);
        limitsy[0] = -height / 2;
    }
    ImageProcessor ip = new ByteProcessor(width, height);
    // Adjust x and y using the minimum to centre
    x[0] -= limitsx[0];
    y[0] -= limitsy[0];
    for (int j = 1; j < totalSteps; j++) {
        // Adjust x and y using the minimum to centre
        x[j] -= limitsx[0];
        y[j] -= limitsy[0];
        // Draw a line
        ip.setColor(32 + (223 * j) / (totalSteps - 1));
        ip.drawLine(round(x[j - 1]), round(y[j - 1]), round(x[j]), round(y[j]));
    }
    // Draw the final position
    ip.putPixel((int) round(x[totalSteps - 1]), (int) round(y[totalSteps - 1]), 255);
    ImagePlus imp = Utils.display(TITLE + " example", ip);
    // Apply the fire lookup table
    WindowManager.setTempCurrentImage(imp);
    LutLoader lut = new LutLoader();
    lut.run("fire");
    WindowManager.setTempCurrentImage(null);
}

Example 4 with LutLoader

use of ij.plugin.LutLoader in project GDSC-SMLM by aherbert.

the class TraceMolecules method showPlot.

/**
	 * Shows the plot
	 */
private void showPlot() {
    if (settings.getOptimiserPlot() == OptimiserPlot.NONE)
        return;
    // Display the image
    String title = TITLE + ": | N - N_actual | / N_actual";
    ImagePlus imp = WindowManager.getImage(title);
    if (imp != null) {
        fp.setColorModel(imp.getProcessor().getColorModel());
        imp.setProcessor(fp);
    } else {
        imp = new ImagePlus(title, fp);
        imp.show();
        WindowManager.setTempCurrentImage(imp);
        LutLoader lut = new LutLoader();
        lut.run("fire");
        WindowManager.setTempCurrentImage(null);
    }
    imp.setCalibration(cal);
    addZeroCrossingPoints(imp);
    imp.updateAndDraw();
}

Example 5 with LutLoader

use of ij.plugin.LutLoader in project GDSC-SMLM by aherbert.

the class TraceMolecules method showPlot.

/**
 * Shows the plot.
 */
private void showPlot() {
    if (OptimiserPlot.get(settings.getOptimiserPlot()) == OptimiserPlot.NONE) {
        return;
    }
    // Display the image
    final String title = pluginTitle + ": | N - N_actual | / N_actual";
    ImagePlus imp = WindowManager.getImage(title);
    if (imp != null) {
        fp.setColorModel(imp.getProcessor().getColorModel());
        imp.setProcessor(fp);
    } else {
        imp = new ImagePlus(title, fp);
        imp.show();
        WindowManager.setTempCurrentImage(imp);
        final LutLoader lut = new LutLoader();
        lut.run("fire");
        WindowManager.setTempCurrentImage(null);
    }
    imp.setCalibration(cal);
    addZeroCrossingPoints(imp);
    imp.updateAndDraw();
}