Examples with FloatProcessor ij.process.FloatProcessor used on opensource projects

Example 6 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method noInterpolateUpInXAtImageEdge.

@Test
public void noInterpolateUpInXAtImageEdge() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 2.5f, 1.5f, 2);
    fp.putPixelValue(2, 1, 2);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}

Example 7 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method noInterpolateUpInYAtImageEdge.

@Test
public void noInterpolateUpInYAtImageEdge() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 1.5f, 2.5f, 2);
    fp.putPixelValue(1, 2, 2);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}

Example 8 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class IJImagePeakResultsTest method canInterpolateDownInXYAtPixelEdge.

@Test
public void canInterpolateDownInXYAtPixelEdge() {
    IJImagePeakResults r = new IJImagePeakResults(title, bounds, 1);
    r.setDisplayFlags(IJImagePeakResults.DISPLAY_WEIGHTED);
    FloatProcessor fp = new FloatProcessor(bounds.width, bounds.height);
    begin(r);
    addValue(r, 1f, 1f, 4);
    fp.putPixelValue(0, 0, 1f);
    fp.putPixelValue(0, 1, 1f);
    fp.putPixelValue(1, 0, 1f);
    fp.putPixelValue(1, 1, 1f);
    r.end();
    float[] expecteds = getImage(fp);
    float[] actuals = getImage(r);
    Assert.assertArrayEquals(expecteds, actuals, 0);
}

Example 9 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class SpotFinderPreview method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
	 */
public void run(ImageProcessor ip) {
    Rectangle bounds = ip.getRoi();
    MaximaSpotFilter filter = config.createSpotFilter(true);
    // Crop to the ROI
    FloatProcessor fp = ip.crop().toFloat(0, null);
    float[] data = (float[]) fp.getPixels();
    int width = fp.getWidth();
    int height = fp.getHeight();
    Spot[] spots = filter.rank(data, width, height);
    data = filter.getPreprocessedData();
    fp = new FloatProcessor(width, height, data);
    ip = ip.duplicate();
    ip.insert(fp, bounds.x, bounds.y);
    //ip.resetMinAndMax();
    ip.setMinAndMax(fp.getMin(), fp.getMax());
    Overlay o = new Overlay();
    o.add(new ImageRoi(0, 0, ip));
    if (label != null) {
        // Get results for frame
        Coordinate[] actual = ResultsMatchCalculator.getCoordinates(actualCoordinates, imp.getCurrentSlice());
        Coordinate[] predicted = new Coordinate[spots.length];
        for (int i = 0; i < spots.length; i++) {
            predicted[i] = new BasePoint(spots[i].x + bounds.x, spots[i].y + bounds.y);
        }
        // Q. Should this use partial scoring with multi-matches allowed.
        // If so then this needs to be refactored out of the BenchmarkSpotFilter class.
        // TODO - compute AUC and max jaccard and plot			
        // Compute matches
        List<PointPair> matches = new ArrayList<PointPair>(Math.min(actual.length, predicted.length));
        List<Coordinate> FP = new ArrayList<Coordinate>(predicted.length);
        MatchResult result = MatchCalculator.analyseResults2D(actual, predicted, distance * fitConfig.getInitialPeakStdDev0(), null, FP, null, matches);
        // Show scores
        setLabel(String.format("P=%s, R=%s, J=%s", Utils.rounded(result.getPrecision()), Utils.rounded(result.getRecall()), Utils.rounded(result.getJaccard())));
        // Create Rois for TP and FP
        if (showTP) {
            float[] x = new float[matches.size()];
            float[] y = new float[x.length];
            int n = 0;
            for (PointPair pair : matches) {
                BasePoint p = (BasePoint) pair.getPoint2();
                x[n] = p.getX() + 0.5f;
                y[n] = p.getY() + 0.5f;
                n++;
            }
            addRoi(0, o, x, y, n, Color.green);
        }
        if (showFP) {
            float[] x = new float[predicted.length - matches.size()];
            float[] y = new float[x.length];
            int n = 0;
            for (Coordinate c : FP) {
                BasePoint p = (BasePoint) c;
                x[n] = p.getX() + 0.5f;
                y[n] = p.getY() + 0.5f;
                n++;
            }
            addRoi(0, o, x, y, n, Color.red);
        }
    } else {
        float[] x = new float[spots.length];
        float[] y = new float[x.length];
        for (int i = 0; i < spots.length; i++) {
            x[i] = spots[i].x + bounds.x + 0.5f;
            y[i] = spots[i].y + bounds.y + 0.5f;
        }
        PointRoi roi = new PointRoi(x, y);
        // Add options to configure colour and labels
        o.add(roi);
    }
    imp.setOverlay(o);
}

Example 10 with FloatProcessor

use of ij.process.FloatProcessor in project GDSC-SMLM by aherbert.

the class CreateData method updateArea.

private void updateArea(int[] mask, int w, int h) {
    // Note: The apparent area will be bigger due to the PSF width blurring the edges.
    // Assume the entire max intensity mask is in focus and the PSF is Gaussian in the focal plane.
    // Blur the mask
    float[] pixels = new float[mask.length];
    for (int i = 0; i < pixels.length; i++) pixels[i] = mask[i];
    GaussianFilter blur = new GaussianFilter();
    final double scaleX = (double) settings.size / w;
    final double scaleY = (double) settings.size / h;
    // Allow extra?
    double extra = 1;
    double sd = getPsfSD() * extra;
    blur.convolve(pixels, w, h, sd / scaleX, sd / scaleY);
    // Count pixels in blurred mask. Ignore those that are very faint (at the edge of the region)
    int c = 0;
    //		// By fraction of max value
    //		float limit = 0.1f;
    //		//float min = (float) (Maths.max(pixels) * limit);
    //		float min = limit;
    //		for (float f : pixels)
    //			if (f > min)
    //				c++;
    //		// Rank in order and get fraction of sum
    //		Arrays.sort(pixels);
    //		double sum = 0;
    //		double stop = Maths.sum(pixels) * 0.95;
    //		float after = Maths.max(pixels) + 1;
    //		for (float f : pixels)
    //		{
    //			sum += f;
    //			if (sum > stop)
    //			{
    //				break;
    //				//after = f;
    //				//stop = Float.POSITIVE_INFINITY;
    //			}
    //			if (f > after)
    //				break;
    //			c++;
    //		}
    // Threshold to a mask
    FloatProcessor fp = new FloatProcessor(w, h, pixels);
    ShortProcessor sp = (ShortProcessor) fp.convertToShort(true);
    final int t = AutoThreshold.getThreshold(AutoThreshold.Method.OTSU, sp.getHistogram());
    //Utils.display("Blurred", fp);
    for (int i = 0; i < mask.length; i++) if (sp.get(i) >= t)
        c++;
    // Convert 
    final double scale = ((double) c) / mask.length;
    //System.out.printf("Scale = %f\n", scale);
    areaInUm = scale * settings.size * settings.pixelPitch * settings.size * settings.pixelPitch / 1e6;
}