Examples with Color java.awt.Color used on opensource projects

Example 86 with Color

use of java.awt.Color in project GDSC-SMLM by aherbert.

the class FIRE method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Compute the resolution using Fourier Ring Correlation");
    gd.addHelp(About.HELP_URL);
    boolean single = results2 == null;
    gd.addMessage("Image construction options:");
    gd.addChoice("Image_scale", SCALE_ITEMS, SCALE_ITEMS[imageScaleIndex]);
    gd.addChoice("Auto_image_size", IMAGE_SIZE_ITEMS, IMAGE_SIZE_ITEMS[imageSizeIndex]);
    if (extraOptions)
        gd.addCheckbox("Use_signal (if present)", useSignal);
    gd.addNumericField("Max_per_bin", maxPerBin, 0);
    gd.addMessage("Fourier options:");
    String[] fourierMethodNames = SettingsManager.getNames((Object[]) FRC.FourierMethod.values());
    gd.addChoice("Fourier_method", fourierMethodNames, fourierMethodNames[fourierMethodIndex]);
    String[] samplingMethodNames = SettingsManager.getNames((Object[]) FRC.SamplingMethod.values());
    gd.addChoice("Sampling_method", samplingMethodNames, samplingMethodNames[samplingMethodIndex]);
    gd.addSlider("Sampling_factor", 0.2, 4, perimeterSamplingFactor);
    gd.addMessage("FIRE options:");
    String[] thresholdMethodNames = SettingsManager.getNames((Object[]) FRC.ThresholdMethod.values());
    gd.addChoice("Threshold_method", thresholdMethodNames, thresholdMethodNames[thresholdMethodIndex]);
    gd.addCheckbox("Show_FRC_curve", showFRCCurve);
    if (single) {
        gd.addMessage("For single datasets:");
        Label l = (Label) gd.getMessage();
        gd.addNumericField("Block_size", blockSize, 0);
        gd.addCheckbox("Random_split", randomSplit);
        gd.addNumericField("Repeats", repeats, 0);
        gd.addCheckbox("Show_FRC_curve_repeats", showFRCCurveRepeats);
        gd.addCheckbox("Show_FRC_time_evolution", showFRCTimeEvolution);
        gd.addCheckbox("Spurious correlation correction", spuriousCorrelationCorrection);
        gd.addNumericField("Q-value", qValue, 3);
        gd.addNumericField("Precision_Mean", mean, 2, 6, "nm");
        gd.addNumericField("Precision_Sigma", sigma, 2, 6, "nm");
        if (extraOptions)
            gd.addNumericField("Threads", getLastNThreads(), 0);
        // Rearrange the dialog
        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;
    imageScaleIndex = gd.getNextChoiceIndex();
    imageSizeIndex = gd.getNextChoiceIndex();
    if (extraOptions)
        myUseSignal = useSignal = gd.getNextBoolean();
    maxPerBin = Math.abs((int) gd.getNextNumber());
    fourierMethodIndex = gd.getNextChoiceIndex();
    fourierMethod = FourierMethod.values()[fourierMethodIndex];
    samplingMethodIndex = gd.getNextChoiceIndex();
    samplingMethod = SamplingMethod.values()[samplingMethodIndex];
    perimeterSamplingFactor = gd.getNextNumber();
    thresholdMethodIndex = gd.getNextChoiceIndex();
    thresholdMethod = FRC.ThresholdMethod.values()[thresholdMethodIndex];
    showFRCCurve = gd.getNextBoolean();
    if (single) {
        blockSize = Math.max(1, (int) gd.getNextNumber());
        randomSplit = gd.getNextBoolean();
        repeats = Math.max(1, (int) gd.getNextNumber());
        showFRCCurveRepeats = gd.getNextBoolean();
        showFRCTimeEvolution = gd.getNextBoolean();
        spuriousCorrelationCorrection = gd.getNextBoolean();
        qValue = Math.abs(gd.getNextNumber());
        mean = Math.abs(gd.getNextNumber());
        sigma = Math.abs(gd.getNextNumber());
        if (extraOptions) {
            setThreads((int) gd.getNextNumber());
            lastNThreads = this.nThreads;
        }
    }
    // Check arguments
    try {
        Parameters.isAboveZero("Perimeter sampling factor", perimeterSamplingFactor);
        if (single && spuriousCorrelationCorrection) {
            Parameters.isAboveZero("Q-value", qValue);
            Parameters.isAboveZero("Precision Mean", mean);
            Parameters.isAboveZero("Precision Sigma", sigma);
            // Set these for use in FIRE computation 
            setCorrectionParameters(qValue, mean, sigma);
        }
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}

Example 87 with Color

use of java.awt.Color 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 88 with Color

use of java.awt.Color in project GDSC-SMLM by aherbert.

the class GaussianFit method setOverlay.

/**
	 * Show the points as an overlay
	 * 
	 * @param nMaxima
	 * @param xpoints
	 * @param ypoints
	 */
private void setOverlay(int nMaxima, int[] xpoints, int[] ypoints) {
    PointRoi roi = new PointRoi(xpoints, ypoints, nMaxima);
    Color strokeColor = Color.yellow;
    Color fillColor = Color.green;
    roi.setStrokeColor(strokeColor);
    roi.setFillColor(fillColor);
    roi.setShowLabels(false);
    imp.setOverlay(roi, strokeColor, 2, fillColor);
}

Example 89 with Color

use of java.awt.Color 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;
}

Example 90 with Color

use of java.awt.Color in project aima-java by aimacode.

the class MapViewPane method paintPreview.

/**
	 * Draws the off-screen image if exists at position (dx, dy) scaled by the
	 * specified factor.
	 */
private void paintPreview(int dx, int dy, float zoomfactor) {
    if (image != null) {
        Graphics2D g2 = (Graphics2D) getGraphics();
        UColor bg = getRenderer().getBackgroundColor();
        g2.setBackground(new Color(bg.getRed(), bg.getGreen(), bg.getBlue(), bg.getAlpha()));
        int newWidth = Math.round(image.getWidth(null) * zoomfactor);
        int newHeight = (int) Math.round(image.getHeight(null) * zoomfactor);
        g2.drawImage(image, dx, dy, newWidth, newHeight, null);
        if (dx > 0)
            g2.clearRect(0, 0, dx, getHeight());
        else
            g2.clearRect(getWidth() + dx, 0, getWidth(), getHeight());
        if (dy > 0)
            g2.clearRect(0, 0, getWidth(), dy);
        else
            g2.clearRect(0, getHeight() + dy, getWidth(), getHeight());
    }
}