Examples with GenericDialog ij.gui.GenericDialog used on opensource projects

Example 1 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class PSFDrift method showHWHM.

private void showHWHM(List<String> titles) {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Select the input PSF image");
    gd.addChoice("PSF", titles.toArray(new String[titles.size()]), title);
    gd.addCheckbox("Use_offset", useOffset);
    gd.addNumericField("Scale", scale, 2);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    title = gd.getNextChoice();
    useOffset = gd.getNextBoolean();
    scale = gd.getNextNumber();
    imp = WindowManager.getImage(title);
    if (imp == null) {
        IJ.error(TITLE, "No PSF image for image: " + title);
        return;
    }
    psfSettings = getPSFSettings(imp);
    if (psfSettings == null) {
        IJ.error(TITLE, "No PSF settings for image: " + title);
        return;
    }
    int size = imp.getStackSize();
    ImagePSFModel psf = createImagePSF(1, size);
    double[] w0 = psf.getAllHWHM0();
    double[] w1 = psf.getAllHWHM1();
    double[] slice = Utils.newArray(w0.length, 1, 1.0);
    // Widths are in pixels
    String title = TITLE + " HWHM";
    Plot plot = new Plot(title, "Slice", "HWHM (px)");
    double[] limits = Maths.limits(w0);
    limits = Maths.limits(limits, w1);
    plot.setLimits(1, size, 0, limits[1] * 1.05);
    plot.setColor(Color.red);
    plot.addPoints(slice, w0, Plot.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(slice, w1, Plot.LINE);
    plot.setColor(Color.black);
    plot.addLabel(0, 0, "X=red; Y=blue");
    Utils.display(title, plot);
}

Example 2 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class PSFCombiner method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    // Build a list of suitable images
    titles = createImageList();
    if (titles.isEmpty()) {
        IJ.error(TITLE, "No suitable PSF images");
        return;
    }
    try {
        while (selectNextImage()) ;
    } catch (Exception e) {
        IJ.error(TITLE, e.getMessage());
        return;
    }
    if (input.isEmpty()) {
        return;
    }
    if (input.size() < 2) {
        IJ.error(TITLE, "Require at least 2 PSF images to combine");
        return;
    }
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Set the maximum z-depth +/- from the PSF centre");
    gd.addSlider("Z-depth", 20, 200, zDepth);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    zDepth = Math.abs((int) gd.getNextNumber());
    for (PSF psf : input) psf.crop(zDepth);
    combineImages();
}

Example 3 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class GaussianFit method showDialog.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.ExtendedPlugInFilter#showDialog(ij.ImagePlus, java.lang.String,
	 * ij.plugin.filter.PlugInFilterRunner)
	 */
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    double[] limits = getLimits(imp.getProcessor());
    double minValue = limits[0];
    double maxValue = limits[1];
    if (background > maxValue)
        background = (int) maxValue;
    if (background < minValue)
        background = (int) minValue;
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Fit 2D Gaussian to identified maxima");
    gd.addMessage("--- Image smoothing ---\n" + "- Within a 2n+1 box\n");
    gd.addSlider("Smoothing", 0, 4.5, smooth);
    gd.addMessage("--- Maxima identification ---\n" + "- Within a 2n+1 box\n");
    gd.addSlider("Box_size", 1, 15, boxSize);
    gd.addSlider("Background", minValue, maxValue, background);
    gd.addSlider("Min_height", 0, maxValue, peakHeight);
    gd.addSlider("Fraction_above_background", 0, 1.01, fractionAboveBackground);
    gd.addSlider("Min_width", 0, 20, peakWidth);
    gd.addSlider("Top_N", 0, 20, topN);
    gd.addCheckbox("Block_find_algorithm", blockFindAlgorithm);
    gd.addCheckbox("Neighbour_check", neighbourCheck);
    gd.addSlider("Border", 0, 15, border);
    gd.addMessage("--- Gaussian fitting ---");
    Component splitLabel = gd.getMessage();
    String[] functionNames = SettingsManager.getNames((Object[]) FitFunction.values());
    gd.addChoice("Fit_function", functionNames, functionNames[fitFunction]);
    gd.addCheckbox("Fit_background", fitBackground);
    String[] criteriaNames = SettingsManager.getNames((Object[]) FitCriteria.values());
    gd.addChoice("Fit_criteria", criteriaNames, criteriaNames[fitCriteria]);
    gd.addNumericField("Max_iterations", maxIterations, 0);
    gd.addNumericField("Significant_digits", significantDigits, 0);
    gd.addNumericField("Coord_delta", delta, 4);
    gd.addCheckbox("Single_fit", singleFit);
    gd.addNumericField("Single_region_size", singleRegionSize, 0);
    gd.addNumericField("Initial_StdDev", initialPeakStdDev, 3);
    gd.addCheckbox("Log_progress", logProgress);
    gd.addCheckbox("Show_deviations", showDeviations);
    gd.addCheckbox("Filter_results", filterResults);
    gd.addCheckbox("Show_fit", showFit);
    gd.addPreviewCheckbox(pfr);
    gd.addDialogListener(this);
    if (gd.getLayout() != null) {
        GridBagLayout grid = (GridBagLayout) gd.getLayout();
        int xOffset = 0, yOffset = 0;
        int lastY = -1, rowCount = 0;
        for (Component comp : gd.getComponents()) {
            // Check if this should be the second major column
            if (comp == splitLabel) {
                xOffset += 2;
                yOffset -= rowCount;
            }
            // Reposition the field
            GridBagConstraints c = grid.getConstraints(comp);
            if (lastY != c.gridy)
                rowCount++;
            lastY = c.gridy;
            c.gridx = c.gridx + xOffset;
            c.gridy = c.gridy + yOffset;
            c.insets.left = c.insets.left + 10 * xOffset;
            c.insets.top = 0;
            c.insets.bottom = 0;
            grid.setConstraints(comp, c);
        }
        if (IJ.isLinux())
            gd.setBackground(new Color(238, 238, 238));
    }
    gd.showDialog();
    if (gd.wasCanceled() || !dialogItemChanged(gd, null)) {
        //			imp.getProcessor().reset();
        imp.setOverlay(null);
        return DONE;
    }
    return flags;
}

Example 4 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class LoadLocalisations method getZDepth.

private boolean getZDepth(MemoryPeakResults results) {
    // The z-depth is stored in pixels in the error field
    double min = results.getHead().error;
    double max = min;
    for (PeakResult peak : results.getResults()) {
        if (min > peak.error)
            min = peak.error;
        else if (max < peak.error)
            max = peak.error;
    }
    // No z-depth
    if (min == max && min == 0)
        return true;
    maxz = FastMath.min(maxz, max);
    minz = FastMath.max(minz, min);
    // Display in nm
    final double pp = results.getNmPerPixel();
    min *= pp;
    max *= pp;
    String msg = String.format("%d localisations with %.2f <= z <= %.2f", results.size(), min, max);
    min = Math.floor(min);
    max = Math.ceil(max);
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage(msg);
    gd.addCheckbox("Limit Z-depth", limitZ);
    gd.addSlider("minZ", min, max, minz * pp);
    gd.addSlider("maxZ", min, max, maxz * pp);
    gd.showDialog();
    if (gd.wasCanceled() || gd.invalidNumber()) {
        return false;
    }
    myLimitZ = limitZ = gd.getNextBoolean();
    minz = gd.getNextNumber() / pp;
    maxz = gd.getNextNumber() / pp;
    return true;
}

Example 5 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class LoadLocalisations method getFields.

private static boolean getFields() {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Load delimited localisations");
    gd.addStringField("Dataset_name", name, 30);
    gd.addMessage("Calibration:");
    gd.addNumericField("Pixel_size", pixelPitch, 3, 8, "nm");
    gd.addNumericField("Gain", gain, 3, 8, "Count/photon");
    gd.addNumericField("Exposure_time", exposureTime, 3, 8, "ms");
    gd.addMessage("Records:");
    gd.addNumericField("Header_lines", header, 0);
    gd.addStringField("Comment", comment);
    gd.addStringField("Delimiter", delimiter);
    String[] dUnits = SettingsManager.getNames((Object[]) DistanceUnit.values());
    gd.addChoice("Distance_unit", dUnits, dUnits[distanceUnit]);
    String[] iUnits = SettingsManager.getNames((Object[]) IntensityUnit.values());
    gd.addChoice("Intensity_unit", iUnits, iUnits[intensityUnit]);
    gd.addMessage("Define the fields:");
    Label l = (Label) gd.getMessage();
    gd.addNumericField("T", it, 0);
    gd.addNumericField("ID", iid, 0);
    gd.addNumericField("X", ix, 0);
    gd.addNumericField("Y", iy, 0);
    gd.addNumericField("Z", iz, 0);
    gd.addNumericField("Intensity", ii, 0);
    gd.addNumericField("Sx", isx, 0);
    gd.addNumericField("Sy", isy, 0);
    gd.addNumericField("Precision", ip, 0);
    // Rearrange
    if (gd.getLayout() != null) {
        GridBagLayout grid = (GridBagLayout) gd.getLayout();
        int xOffset = 0, yOffset = 0;
        int lastY = -1, rowCount = 0;
        for (Component comp : gd.getComponents()) {
            // Check if this should be the second major column
            if (comp == l) {
                xOffset += 2;
                // Skip title row
                yOffset = yOffset - rowCount + 1;
            }
            // Reposition the field
            GridBagConstraints c = grid.getConstraints(comp);
            if (lastY != c.gridy)
                rowCount++;
            lastY = c.gridy;
            c.gridx = c.gridx + xOffset;
            c.gridy = c.gridy + yOffset;
            c.insets.left = c.insets.left + 10 * xOffset;
            c.insets.top = 0;
            c.insets.bottom = 0;
            grid.setConstraints(comp, c);
        }
        if (IJ.isLinux())
            gd.setBackground(new Color(238, 238, 238));
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    name = getNextString(gd, name);
    pixelPitch = gd.getNextNumber();
    gain = gd.getNextNumber();
    exposureTime = gd.getNextNumber();
    header = (int) gd.getNextNumber();
    comment = gd.getNextString();
    delimiter = getNextString(gd, delimiter);
    distanceUnit = gd.getNextChoiceIndex();
    intensityUnit = gd.getNextChoiceIndex();
    int[] columns = new int[9];
    for (int i = 0; i < columns.length; i++) columns[i] = (int) gd.getNextNumber();
    {
        int i = 0;
        it = columns[i++];
        iid = columns[i++];
        ix = columns[i++];
        iy = columns[i++];
        iz = columns[i++];
        ii = columns[i++];
        isx = columns[i++];
        isy = columns[i++];
        ip = columns[i++];
    }
    if (gd.invalidNumber()) {
        IJ.error(TITLE, "Invalid number in input fields");
        return false;
    }
    for (int i = 0; i < columns.length; i++) {
        if (columns[i] < 0)
            continue;
        for (int j = i + 1; j < columns.length; j++) {
            if (columns[j] < 0)
                continue;
            if (columns[i] == columns[j]) {
                IJ.error(TITLE, "Duplicate indicies: " + columns[i]);
                return false;
            }
        }
    }
    if (gain <= 0 || pixelPitch <= 0) {
        IJ.error(TITLE, "Require positive gain and pixel pitch");
        return false;
    }
    if (ix < 0 || iy < 0) {
        IJ.error(TITLE, "Require valid X and Y indices");
        return false;
    }
    return true;
}