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

Example 6 with Roi

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

the class EMGainAnalysis method buildHistogram.

/**
	 * Build a histogram using pixels within the image ROI
	 * 
	 * @param image
	 *            The image
	 * @return The image histogram
	 */
private static int[] buildHistogram(ImagePlus imp) {
    ImageStack stack = imp.getImageStack();
    Roi roi = imp.getRoi();
    int[] data = getHistogram(stack.getProcessor(1), roi);
    for (int n = 2; n <= stack.getSize(); n++) {
        int[] tmp = getHistogram(stack.getProcessor(n), roi);
        for (int i = 0; i < tmp.length; i++) data[i] += tmp[i];
    }
    // Avoid super-saturated pixels by using 98% of histogram
    long sum = 0;
    for (int i = 0; i < data.length; i++) {
        sum += data[i];
    }
    final long sum2 = (long) (sum * 0.99);
    sum = 0;
    for (int i = 0; i < data.length; i++) {
        sum += data[i];
        if (sum > sum2) {
            for (; i < data.length; i++) data[i] = 0;
            break;
        }
    }
    return data;
}

Example 7 with Roi

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

the class PSFCreator method ignoreSpot.

private boolean ignoreSpot(int n, final double[] z, final double[] a, final double[] smoothA, final double[] xCoord, final double[] yCoord, final double[] sd, final double[] newZ, final double[] smoothX, final double[] smoothY, double[] smoothSd, final double cx, final double cy, final int cz, double csd) {
    this.slice = cz;
    // the addition of the data
    if (interactiveMode) {
        zCentre = cz;
        psfWidth = csd * nmPerPixel;
        // Store the data for replotting
        this.z = z;
        this.a = a;
        this.smoothAz = z;
        this.smoothA = smoothA;
        this.xCoord = xCoord;
        this.yCoord = yCoord;
        this.sd = sd;
        this.newZ = newZ;
        this.smoothX = smoothX;
        this.smoothY = smoothY;
        this.smoothSd = smoothSd;
        showPlots(z, a, z, smoothA, xCoord, yCoord, sd, newZ, smoothX, smoothY, smoothSd, cz);
        // Draw the region on the input image as an overlay
        imp.setSlice(cz);
        imp.setOverlay(new Roi((int) (cx - boxRadius), (int) (cy - boxRadius), 2 * boxRadius + 1, 2 * boxRadius + 1), Color.GREEN, 1, null);
        // Ask if the spot should be included
        GenericDialog gd = new GenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage(String.format("Add spot %d to the PSF?\n \nEstimated centre using min PSF width:\n \nx = %.2f\ny = %.2f\nz = %d\nsd = %.2f\n", n, cx, cy, cz, csd));
        gd.addSlider("Slice", z[0], z[z.length - 1], slice);
        if (yesNoPosition != null) {
            gd.centerDialog(false);
            gd.setLocation(yesNoPosition);
        }
        gd.addDialogListener(new SimpleInteractivePlotListener());
        gd.showDialog();
        yesNoPosition = gd.getLocation();
        return !gd.wasOKed();
    }
    return false;
}

Example 8 with Roi

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

the class OverlayImage method addImage.

/**
	 * Adapted from ij.plugins.OverlayCommands#addImage(boolean) with the additional option for setting the zero pixels
	 * to transparent.
	 */
void addImage() {
    ImagePlus imp = IJ.getImage();
    int[] wList = WindowManager.getIDList();
    if (wList == null || wList.length < 2) {
        IJ.error("Add Image...", "The command requires at least two open images.");
        return;
    }
    String[] titles = new String[wList.length];
    int count = 0;
    for (int i = 0; i < wList.length; i++) {
        ImagePlus imp2 = WindowManager.getImage(wList[i]);
        if (imp2 != null && imp2 != imp && imp.getWidth() >= imp2.getWidth() && imp.getHeight() >= imp2.getHeight())
            titles[count++] = imp2.getTitle();
    }
    if (count < 1) {
        IJ.error("Add Image...", "The command requires at least one valid overlay image.");
        return;
    }
    titles = Arrays.copyOf(titles, count);
    int x = 0, y = 0;
    Roi roi = imp.getRoi();
    if (roi != null && roi.isArea()) {
        Rectangle r = roi.getBounds();
        x = r.x;
        y = r.y;
    }
    GenericDialog gd = new GenericDialog("Add Image...");
    gd.addChoice("Image to add:", titles, title);
    gd.addNumericField("X location:", x, 0);
    gd.addNumericField("Y location:", y, 0);
    gd.addNumericField("Opacity (0-100%):", opacity, 0);
    gd.addCheckbox("Transparent background", transparent);
    gd.addCheckbox("Replace overlay", replace);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    title = gd.getNextChoice();
    x = (int) gd.getNextNumber();
    y = (int) gd.getNextNumber();
    opacity = (int) gd.getNextNumber();
    transparent = gd.getNextBoolean();
    replace = gd.getNextBoolean();
    ImagePlus overlay = WindowManager.getImage(title);
    if (overlay == imp) {
        IJ.error("Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
        return;
    }
    if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
        IJ.error("Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
        return;
    }
    ImageRoi roi2 = new ImageRoi(x, y, overlay.getProcessor());
    roi2.setZeroTransparent(transparent);
    roi2.setName(overlay.getShortTitle());
    if (opacity != 100)
        roi2.setOpacity(opacity / 100.0);
    Overlay overlayList = imp.getOverlay();
    if (overlayList == null || replace)
        overlayList = new Overlay();
    overlayList.add(roi2);
    imp.setOverlay(overlayList);
    Undo.setup(Undo.OVERLAY_ADDITION, imp);
}

Example 9 with Roi

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

the class PSFCreator method setup.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
	 */
public int setup(String arg, ImagePlus imp) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (imp == null) {
        IJ.noImage();
        return DONE;
    }
    Roi roi = imp.getRoi();
    if (roi == null || roi.getType() != Roi.POINT) {
        IJ.error("Point ROI required");
        return DONE;
    }
    this.imp = imp;
    return showDialog();
}

Example 10 with Roi

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

the class PSFCreator method getSpots.

/**
	 * @return Extract all the ROI points that are not within twice the box radius of any other spot
	 */
private BasePoint[] getSpots() {
    Roi roi = imp.getRoi();
    if (roi != null && roi.getType() == Roi.POINT) {
        Polygon p = ((PolygonRoi) roi).getNonSplineCoordinates();
        int n = p.npoints;
        Rectangle bounds = roi.getBounds();
        BasePoint[] roiPoints = new BasePoint[n];
        for (int i = 0; i < n; i++) {
            roiPoints[i] = new BasePoint(bounds.x + p.xpoints[i], bounds.y + p.ypoints[i], 0);
        }
        // All vs all distance matrix
        double[][] d = new double[n][n];
        for (int i = 0; i < n; i++) for (int j = i + 1; j < n; j++) d[i][j] = d[j][i] = roiPoints[i].distanceXY2(roiPoints[j]);
        // Spots must be twice as far apart to have no overlap of the extracted box region
        double d2 = boxRadius * boxRadius * 4;
        int ok = 0;
        for (int i = 0; i < n; i++) {
            if (noNeighbours(d, n, i, d2))
                roiPoints[ok++] = roiPoints[i];
        }
        return Arrays.copyOf(roiPoints, ok);
    }
    return new BasePoint[0];
}