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

Example 11 with Roi

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

the class EMGainAnalysis method run.

public void run(ImageProcessor ip) {
    // Calculate the histogram
    final int[] h = (simulate) ? simulateHistogram(usePDF ? 0 : 1) : buildHistogram(imp);
    // We need > 10^7 pixels from flat white-light images under constant exposure ...
    final int size = getSize(h);
    if (imp != null) {
        Roi roi = imp.getRoi();
        Rectangle bounds;
        if (roi == null)
            bounds = new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
        else
            bounds = roi.getBounds();
        Utils.log("Analysing %s [x=%d,y=%d,width=%d,height=%d]", imp.getTitle(), bounds.x, bounds.y, bounds.width, bounds.height);
    }
    Utils.log("Histogram contains %d pixels", size);
    if (size < MINIMUM_PIXELS)
        Utils.log("WARNING : Recommend at least %d pixels (%sx more)", MINIMUM_PIXELS, Utils.rounded((double) MINIMUM_PIXELS / size));
    fit(h);
}

Example 12 with Roi

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

the class DriftCalculator method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    // Require some fit results and selected regions
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    Roi[] rois = getRois();
    String[] stackTitles = createStackImageList();
    if (!showDialog(rois, stackTitles))
        return;
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() < 2) {
        IJ.error(TITLE, "There are not enough fitting results for drift correction");
        return;
    }
    double[][] drift = null;
    int[] limits = findTimeLimits(results);
    if (method.equals(MARKED_ROIS)) {
        drift = calculateUsingMarkers(results, limits, rois);
    } else if (method.equals(STACK_ALIGNMENT)) {
        ImageStack stack = showStackDialog(stackTitles);
        if (stack == null)
            return;
        drift = calculateUsingImageStack(stack, limits);
    } else if (method.equals(DRIFT_FILE)) {
        drift = calculateUsingDriftFile(limits);
    } else {
        if (!showSubImageDialog())
            return;
        drift = calculateUsingFrames(results, limits, Integer.parseInt(reconstructionSize));
    }
    if (drift == null)
        return;
    Utils.log("Drift correction interpolated for frames [%d - %d] of [%d - %d] (%s%%)", interpolationStart, interpolationEnd, limits[0], limits[1], Utils.rounded((100.0 * (interpolationEnd - interpolationStart + 1)) / (limits[1] - limits[0] + 1)));
    applyDriftCorrection(results, drift);
}

Example 13 with Roi

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

the class SmoothImage method setup.

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

Example 14 with Roi

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

the class PCPALMAnalysis method cropToRoi.

/**
	 * Extract all the PC-PALM molecules that are within the image ROI region. The coordinates bounds are
	 * converted using relative scaling to the limits of the PC-PALM molecules. If a non-rectangular ROI is used then a
	 * mask is extracted and used for the crop. If no image is provided then the full set of molecules is returned.
	 * <p>
	 * Set the area property to the region covered by the molecules.
	 * 
	 * @param imp
	 * @return
	 */
ArrayList<Molecule> cropToRoi(ImagePlus imp) {
    croppedArea = PCPALMMolecules.area;
    if (PCPALMMolecules.molecules == null || PCPALMMolecules.molecules.isEmpty()) {
        return PCPALMMolecules.molecules;
    }
    double pcw = PCPALMMolecules.maxx - PCPALMMolecules.minx;
    double pch = PCPALMMolecules.maxy - PCPALMMolecules.miny;
    Roi roi = (imp == null) ? null : imp.getRoi();
    if (roi == null || !roi.isArea()) {
        log("Roi = %s nm x %s nm = %s um^2", Utils.rounded(pcw, 3), Utils.rounded(pch, 3), Utils.rounded(croppedArea, 3));
        minx = PCPALMMolecules.minx;
        maxx = PCPALMMolecules.maxx;
        miny = PCPALMMolecules.miny;
        maxy = PCPALMMolecules.maxy;
        return PCPALMMolecules.molecules;
    }
    int w = imp.getWidth();
    int h = imp.getHeight();
    Rectangle bounds = roi.getBounds();
    // Construct relative coordinates
    minx = PCPALMMolecules.minx + pcw * ((double) bounds.x / w);
    miny = PCPALMMolecules.miny + pch * ((double) bounds.y / h);
    maxx = PCPALMMolecules.minx + pcw * ((double) (bounds.x + bounds.width) / w);
    maxy = PCPALMMolecules.miny + pch * ((double) (bounds.y + bounds.height) / h);
    final double roix = maxx - minx;
    final double roiy = maxy - miny;
    ArrayList<Molecule> newMolecules = new ArrayList<Molecule>(PCPALMMolecules.molecules.size() / 2);
    // Support non-rectangular ROIs
    if (roi.getMask() != null) {
        MaskDistribution dist = createMaskDistribution(roi.getMask(), roix, roiy);
        double fraction = (double) dist.getSize() / (roi.getMask().getWidth() * roi.getMask().getHeight());
        log("Roi is a mask of %d pixels", dist.getSize());
        croppedArea = fraction * roix * roiy / 1e6;
        log("Roi area %s x %s nm x %s nm = %s um^2", Utils.rounded(fraction), Utils.rounded(roix, 3), Utils.rounded(roiy, 3), Utils.rounded(croppedArea, 3));
        double[] xyz = new double[3];
        // The mask is 0,0 in the centre so offset by this as well
        double xoffset = minx + roix / 2;
        double yoffset = miny + roiy / 2;
        for (Molecule m : PCPALMMolecules.molecules) {
            xyz[0] = m.x - xoffset;
            xyz[1] = m.y - yoffset;
            if (dist.isWithinXY(xyz))
                newMolecules.add(m);
        }
    } else {
        croppedArea = roix * roiy / 1e6;
        log("Roi = %s nm x %s nm = %s um^2", Utils.rounded(roix, 3), Utils.rounded(roiy, 3), Utils.rounded(croppedArea, 3));
        for (Molecule m : PCPALMMolecules.molecules) {
            if (m.x < minx || m.x >= maxx || m.y < miny || m.y >= maxy)
                continue;
            newMolecules.add(m);
        }
    }
    return newMolecules;
}