Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 36 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus imp = this.imp;
    if (fitMaxima && singleFrame > 0) {
        if (source instanceof IJImageSource) {
            String title = source.getName();
            imp = WindowManager.getImage(title);
        }
    }
    if (singleFrame > 0 && imp != null) {
        MemoryPeakResults results = null;
        for (PeakResults r : this.results.toArray()) if (r instanceof MemoryPeakResults) {
            results = (MemoryPeakResults) r;
            break;
        }
        if (results == null || results.size() == 0)
            return;
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        LUT lut = LUTHelper.createLUT(LutColour.ICE);
        Overlay o = new Overlay();
        ArrayList<PeakResult> list = (ArrayList<PeakResult>) results.getResults();
        for (int i = 0, j = results.size() - 1; i < results.size(); i++, j--) {
            PeakResult r = list.get(i);
            PointRoi roi = new PointRoi(r.getXPosition(), r.getYPosition());
            Color c = LUTHelper.getColour(lut, j, results.size());
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (imp.getStackSize() > 1)
                roi.setPosition(singleFrame);
            o.add(roi);
        }
        imp.setOverlay(o);
        imp.getWindow().toFront();
    }
}

Example 37 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PeakFit method initialiseFitting.

/**
	 * Set-up the fitting using all the configured properties. Prepare the output results.
	 */
public boolean initialiseFitting() {
    if (source == null)
        return false;
    // Do this to ensure the serialised configuration is correct
    updateFitConfiguration(config);
    results.setSource(source);
    if (maximaIdentification)
        results.setName(source.getName() + " (Maxima)");
    else if (fitMaxima)
        results.setName(source.getName() + " (" + getSolverName() + " Fit Maxima)");
    else
        results.setName(source.getName() + " (" + getSolverName() + ")");
    results.setBounds(bounds);
    Calibration cal = calibration.clone();
    // Account for the frame integration
    // TODO - Should we change this so that if integrate frames is used then the data 
    // are converted to ExtendedPeakResult with a start and end frame
    //cal.exposureTime *= integrateFrames;
    //if (interlacedData)
    //{
    //	cal.exposureTime *= ((double)dataBlock / (dataBlock + dataSkip));
    //}
    results.setCalibration(cal);
    results.setConfiguration(XmlUtils.toXML(config));
    addMemoryResults(results, false);
    addImageResults(results);
    addFileResults(results);
    addTableResults(results);
    addDefaultResults(results);
    results.begin();
    if (simpleFit && showImage) {
        for (PeakResults r : results.toArray()) {
            if (r instanceof IJImagePeakResults) {
                ImagePlus i = ((IJImagePeakResults) r).getImagePlus();
                Utils.log("Super-resolution image title = " + i.getTitle());
                WindowManager.toFront(i.getWindow());
            }
        }
    }
    return true;
}

Example 38 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PCPALMMolecules method createImage.

private boolean createImage(ArrayList<Molecule> molecules) {
    if (molecules.isEmpty())
        return false;
    // Find the limits of the image
    minx = maxx = molecules.get(0).x;
    miny = maxy = molecules.get(0).y;
    // Compute limits
    for (int i = molecules.size(); i-- > 0; ) {
        final Molecule m1 = molecules.get(i);
        if (minx > m1.x)
            minx = m1.x;
        else if (maxx < m1.x)
            maxx = m1.x;
        if (miny > m1.y)
            miny = m1.y;
        else if (maxy < m1.y)
            maxy = m1.y;
    }
    //		// Debug all-vs-all comparison
    //		long start = System.nanoTime();
    //		double dMin2 = Double.POSITIVE_INFINITY;
    //		for (int i = molecules.size(); i-- > 0;)
    //		{
    //			final Molecule m1 = molecules.get(i);
    //			for (int j = i; j-- > 0;)
    //			{
    //				final Molecule m2 = molecules.get(j);
    //				if (dMin2 > m1.distance2(m2))
    //					dMin2 = m1.distance2(m2);
    //			}
    //		}
    //		long t1 = System.nanoTime() - start;
    // Assign to a grid
    final int gridSize = 500;
    final double xBinSize = (maxx - minx) / gridSize;
    final double yBinSize = (maxy - miny) / gridSize;
    final int nXBins = 1 + (int) ((maxx - minx) / xBinSize);
    final int nYBins = 1 + (int) ((maxy - miny) / yBinSize);
    Molecule[][] grid = new Molecule[nXBins][nYBins];
    for (Molecule m : molecules) {
        final int xBin = (int) ((m.x - minx) / xBinSize);
        final int yBin = (int) ((m.y - miny) / yBinSize);
        // Build a single linked list
        m.next = grid[xBin][yBin];
        grid[xBin][yBin] = m;
    }
    // Find the minimum distance between molecules.
    double dMin = Double.POSITIVE_INFINITY;
    IJ.showStatus("Computing minimum distance ...");
    IJ.showProgress(0);
    Molecule[] neighbours = new Molecule[5];
    for (int yBin = 0, currentIndex = 0, finalIndex = nXBins * nYBins; yBin < nYBins; yBin++) {
        for (int xBin = 0; xBin < nXBins; xBin++) {
            IJ.showProgress(currentIndex, finalIndex);
            for (Molecule m1 = grid[xBin][yBin]; m1 != null; m1 = m1.next) {
                // Build a list of which cells to compare up to a maximum of 4
                //      | 0,0  |  1,0
                // ------------+-----
                // -1,1 | 0,1  |  1,1
                int count = 0;
                neighbours[count++] = m1.next;
                if (yBin < nYBins - 1) {
                    neighbours[count++] = grid[xBin][yBin + 1];
                    if (xBin > 0)
                        neighbours[count++] = grid[xBin - 1][yBin + 1];
                }
                if (xBin < nXBins - 1) {
                    neighbours[count++] = grid[xBin + 1][yBin];
                    if (yBin < nYBins - 1)
                        neighbours[count++] = grid[xBin + 1][yBin + 1];
                }
                // Compare to neighbours
                while (count-- > 0) {
                    for (Molecule m2 = neighbours[count]; m2 != null; m2 = m2.next) {
                        if (dMin > m1.distance2(m2))
                            dMin = m1.distance2(m2);
                    }
                }
            }
        }
    }
    IJ.showStatus("");
    IJ.showProgress(1);
    nmPerPixel = Math.sqrt(dMin);
    log("Minimum distance between molecules = %g nm", nmPerPixel);
    if (nmPerPixel == 0 && nmPerPixelLimit == 0) {
        IJ.error(TITLE, "Zero minimum distance between molecules - please enter a nm/pixel limit for image reconstruction");
        return false;
    }
    if (nmPerPixel < nmPerPixelLimit) {
        log("Minimum distance adjusted to user defined limit %.2f nm", nmPerPixelLimit);
        nmPerPixel = nmPerPixelLimit;
    }
    // Compute the minimum size we can use and stay within memory.
    // Assume a 4um x 4um analysis section with 800nm feature radius.
    double limit = (4000.0 + 800.0 + 1) / 4096;
    if (nmPerPixel < limit) {
        log("Minimum distance adjusted to %.2f nm to fit in memory", limit);
        nmPerPixel = limit;
    }
    log("X-range %.2f - %.2f : Y-range %.2f - %.2f (nm)", minx, maxx, miny, maxy);
    // Construct a binary representation
    String namePrefix = results.getName() + " " + ((binaryImage) ? "Binary" : "Count") + " Image";
    double lowResNmPerPixel;
    double xrange = maxx - minx;
    double yrange = maxy - miny;
    if (xrange > 0 || yrange > 0) {
        lowResNmPerPixel = FastMath.max(xrange, yrange) / lowResolutionImageSize;
    } else {
        // The resolution does not matter
        lowResNmPerPixel = 100;
    }
    ImagePlus imp = displayImage(namePrefix + " (low res)", molecules, minx, miny, maxx, maxy, lowResNmPerPixel, false, binaryImage);
    // Add an ROI to allow the user to select regions. PC-PALM recommends 2x2 to 4x4 um^2
    int size = (int) (roiSizeInUm * 1000.0 / lowResNmPerPixel);
    imp.setRoi(new Rectangle(0, 0, size, size));
    if (showHighResolutionImage)
        displayImage(namePrefix + " (high res)", molecules, minx, miny, maxx, maxy, nmPerPixel, false, binaryImage);
    // Store the molecules, the data range and the dMin. 
    // This will be used by a filter plugin that crops sections from the image for PC analysis
    PCPALMMolecules.molecules = molecules;
    return true;
}

Example 39 with ImagePlus

use of ij.ImagePlus 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 40 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class ImageROIPainter method mousePressed.

public void mousePressed(MouseEvent e) {
    // If a multiple-line selection is made then show all the points
    int index = textPanel.getSelectionStart();
    if (index == -1)
        return;
    int index2 = textPanel.getSelectionEnd();
    if (index == index2)
        return;
    ImagePlus imp = WindowManager.getImage(title);
    if (imp == null)
        return;
    // Show all
    int points = 0;
    float[] x = new float[index2 - index + 1];
    float[] y = new float[x.length];
    int[] slice = new int[x.length];
    while (index <= index2) {
        double[] position = coordProvider.getCoordinates(textPanel.getLine(index));
        if (position == null || position.length < 3)
            continue;
        slice[points] = (int) position[0];
        x[points] = (float) position[1];
        y[points] = (float) position[2];
        points++;
        index++;
    }
    if (points == 0)
        return;
    // Simple code to add the ROI onto a single slice: addRoi(imp, slice[0], new PointRoi(x, y, points));
    // Add the ROI to each relevant slice
    // Sort the slices
    int[] indices = new int[points];
    for (int i = 0; i < points; i++) indices[i] = i;
    Sort.sort(indices, slice);
    Overlay o = new Overlay();
    // Create an ROI for each slice
    int start = 0;
    for (int i = 0; i < points; i++) {
        if (slice[indices[i]] != slice[indices[start]]) {
            appendRoi(x, y, slice, indices, o, start, i);
            start = i;
        }
    }
    appendRoi(x, y, slice, indices, o, start, points);
    // Choose the first slice and add the final overlay
    imp.setSlice(slice[indices[start]]);
    if (imp.getWindow() != null)
        imp.getWindow().toFront();
    o.setStrokeColor(Color.green);
    imp.setOverlay(o);
}