Examples with Calibration ij.measure.Calibration used on opensource projects

Example 1 with Calibration

use of ij.measure.Calibration in project GDSC-SMLM by aherbert.

the class PCPALMMolecules method displayImage.

static ImagePlus displayImage(String title, ImageProcessor ip, double nmPerPixel) {
    ImagePlus imp = Utils.display(title, ip);
    Calibration cal = new Calibration();
    cal.setUnit("um");
    cal.pixelWidth = cal.pixelHeight = nmPerPixel / 1000;
    imp.setCalibration(cal);
    return imp;
}

Example 2 with Calibration

use of ij.measure.Calibration 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 3 with Calibration

use of ij.measure.Calibration in project GDSC-SMLM by aherbert.

the class YeastMask method createMask.

private void createMask() {
    // Create the dimensions
    final int hw = (int) Math.ceil(radius * 1000 / nmPerPixel);
    final int hd = (int) Math.ceil(radius * 1000 / nmPerSlice);
    final int width = 2 * hw + 1;
    final int depth = 2 * hd + 1;
    ImageStack stack = createHemiSphere(width, depth);
    // Extend the centre circle of the sphere into a tube of the required length
    final int h = (int) Math.ceil(length * 1000 / nmPerPixel);
    if (h > 0) {
        ImageStack newStack = new ImageStack(width, stack.getHeight() + h, stack.getSize());
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            byte[] pixels = (byte[]) stack.getPixels(slice);
            byte[] newPixels = new byte[width * newStack.getHeight()];
            newStack.setPixels(newPixels, slice);
            System.arraycopy(pixels, 0, newPixels, 0, pixels.length);
            // Get the final strip to be extended
            final int offset = pixels.length - width;
            int target = pixels.length;
            for (int i = 0; i < h; i++) {
                System.arraycopy(pixels, offset, newPixels, target, width);
                target += width;
            }
        }
        stack = newStack;
    }
    // Copy the hemi-sphere onto the end
    ImageStack newStack = new ImageStack(width, stack.getHeight() + hw, stack.getSize());
    for (int slice = 1; slice <= stack.getSize(); slice++) {
        byte[] pixels = (byte[]) stack.getPixels(slice);
        byte[] newPixels = new byte[width * newStack.getHeight()];
        newStack.setPixels(newPixels, slice);
        System.arraycopy(pixels, 0, newPixels, 0, pixels.length);
        // Copy the hemi-sphere
        int source = 0;
        int target = newPixels.length - width;
        for (int i = 0; i < hw; i++) {
            System.arraycopy(pixels, source, newPixels, target, width);
            target -= width;
            source += width;
        }
    }
    stack = newStack;
    if (excludeNucleus) {
        ImageStack stack2 = createNucleusSphere(width, depth);
        int xloc = (stack.getWidth() - stack2.getWidth()) / 2;
        int yloc = (stack.getHeight() - stack2.getHeight()) / 2;
        int offset = (stack.getSize() - stack2.getSize()) / 2;
        for (int slice = 1; slice <= stack2.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice + offset);
            ImageProcessor ip2 = stack2.getProcessor(slice);
            ip.copyBits(ip2, xloc, yloc, Blitter.SUBTRACT);
        }
    }
    if (squareOutput && stack.getWidth() != stack.getHeight()) {
        ImageStack stack2 = new ImageStack(stack.getHeight(), stack.getHeight());
        int end = stack.getHeight() - stack.getWidth();
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice);
            ImageProcessor ip2 = new ByteProcessor(stack2.getWidth(), stack2.getHeight());
            stack2.addSlice(ip2);
            for (int xloc = 0; xloc <= end; xloc += stack.getWidth()) {
                ip2.insert(ip, xloc, 0);
            }
        }
        stack = stack2;
    }
    if (border > 0) {
        ImageStack stack2 = new ImageStack(stack.getWidth() + 2 * border, stack.getHeight() + 2 * border);
        for (int slice = 1; slice <= stack.getSize(); slice++) {
            ImageProcessor ip = stack.getProcessor(slice);
            ImageProcessor ip2 = new ByteProcessor(stack2.getWidth(), stack2.getHeight());
            stack2.addSlice(ip2);
            ip2.insert(ip, border, border);
        }
        stack = stack2;
    }
    ImagePlus imp;
    if (is2D) {
        // TODO - Remove this laziness since we should really just do a 2D image
        int centre = stack.getSize() / 2;
        imp = Utils.display(TITLE, stack.getProcessor(centre));
    } else {
        imp = Utils.display(TITLE, stack);
    }
    // Calibrate
    Calibration cal = new Calibration();
    cal.setUnit("um");
    cal.pixelWidth = cal.pixelHeight = nmPerPixel / 1000;
    cal.pixelDepth = nmPerSlice / 1000;
    imp.setCalibration(cal);
}

Example 4 with Calibration

use of ij.measure.Calibration in project GDSC-SMLM by aherbert.

the class TraceMolecules method addZeroCrossingPoints.

private void addZeroCrossingPoints(ImagePlus imp) {
    PolygonRoi roi = null;
    imp.setRoi(roi);
    if (zeroCrossingPoints == null || zeroCrossingPoints.isEmpty())
        return;
    Calibration cal = imp.getCalibration();
    int nPoints = zeroCrossingPoints.size();
    float[] xPoints = new float[nPoints];
    float[] yPoints = new float[nPoints];
    for (int i = 0; i < nPoints; i++) {
        double[] point = zeroCrossingPoints.get(i);
        // Convert to pixel coordinates. 
        xPoints[i] = (float) (cal.xOrigin + (point[0] / cal.pixelWidth));
        yPoints[i] = (float) (cal.yOrigin + (point[1] / cal.pixelHeight));
    }
    roi = new PolygonRoi(xPoints, yPoints, nPoints, PolygonRoi.POLYLINE);
    imp.setRoi(roi);
}

Example 5 with Calibration

use of ij.measure.Calibration in project GDSC-SMLM by aherbert.

the class TraceMolecules method createPlotResults.

/**
	 * Build an image using the values within the results to set X,Y and value
	 * 
	 * @param results
	 */
private void createPlotResults(List<double[]> results) {
    int w = 400, h = 400;
    switch(settings.getOptimiserPlot()) {
        case NONE:
            return;
        case BILINEAR:
            fp = createBilinearPlot(results, w, h);
            break;
        default:
            fp = createNNPlot(results, w, h);
    }
    // Create a calibration to map the pixel position back to distance/time
    cal = new Calibration();
    double xRange = getRange(settings.maxTimeThreshold, settings.minTimeThreshold, origX, w);
    double yRange = getRange(settings.maxDistanceThreshold, settings.minDistanceThreshold, origY, h);
    cal.pixelWidth = xRange / w;
    cal.pixelHeight = yRange / h;
    cal.xOrigin = origX - settings.minTimeThreshold / cal.pixelWidth;
    cal.yOrigin = origY - settings.minDistanceThreshold / cal.pixelHeight;
    cal.setXUnit("frame");
    cal.setYUnit("pixel");
    showPlot();
}