Examples with NativeType net.imglib2.type.NativeType used on opensource projects

Example 1 with NativeType

use of net.imglib2.type.NativeType in project volumetric-tissue-exploration-analysis by icbm-iupui.

the class Imglib2ConnectedComponents method run.

private <T extends RealType<T>, I extends NumericType<I> & NativeType<I>> void run(ImagePlus imp) {
    OpService ops;
    boolean invert = false;
    ImageJ ij = new ImageJ();
    final Img<I> ImglibOriginal = ImagePlusAdapter.wrap(imp);
    final Img<I> ImglibSegmented = ImglibOriginal.copy();
    final ImgPlus<T> imgSegemented = new ImgPlus(ImglibSegmented);
    Img segmentedImg = (Img) ij.op().threshold().otsu(imgSegemented);
    double tolerance = 5;
    int conn = 26;
    boolean dams = false;
    ImagePlus segmentedImp = ImageJFunctions.wrap((RandomAccessibleInterval<I>) segmentedImg, "Segmented");
    segmentedImp.show();
    ImageStack image = segmentedImp.getImageStack();
    // find regional minima on gradient image with dynamic value of 'tolerance' and 'conn'-connectivity
    ImageStack regionalMinima = MinimaAndMaxima3D.extendedMinima(image, tolerance, conn);
    // impose minima on gradient image
    ImageStack imposedMinima = MinimaAndMaxima3D.imposeMinima(image, regionalMinima, conn);
    // label minima using connected components (32-bit output)
    ImageStack labeledMinima = BinaryImages.componentsLabeling(regionalMinima, conn, 32);
    // apply marker-based watershed using the labeled minima on the minima-imposed
    // gradient image (the last value indicates the use of dams in the output)
    ImageStack resultStack = Watershed.computeWatershed(imposedMinima, labeledMinima, conn, dams);
    ImagePlus watershedImp = new ImagePlus("Wateshed", resultStack);
    watershedImp.show();
    final Img<I> Imglib = ImagePlusAdapter.wrap(watershedImp);
    final ImgPlus<T> img = new ImgPlus(Imglib);
    ImageJFunctions.show(img);
    // 
    // IterableInterval erodedInterval = ij.op().morphology().erode(img, new DiamondShape(1));
    // RandomAccessibleInterval erodedImg = makeRai(erodedInterval, ij);
    ImgLabeling cca = ij.op().labeling().cca(makeRai(img, ij), ConnectedComponents.StructuringElement.EIGHT_CONNECTED);
    // show result
    // ij.ui().show(cca.getIndexImg());
    ImageJFunctions.show(cca.getIndexImg());
    // get count of connected components
    LabelRegions<IntegerType> regions = new LabelRegions(cca);
    int cells = regions.getExistingLabels().size();
    // print result
    System.out.println("Counted " + cells + " cells.");
}

Example 2 with NativeType

use of net.imglib2.type.NativeType in project mia by mianalysis.

the class ManualThreshold method measureSpearman.

public static <T extends RealType<T> & NativeType<T>> HashMap<String, Double> measureSpearman(DataContainer<T> data) {
    // Based on code from
    // https://github.com/fiji/Colocalisation_Analysis/blob/master/src/main/java/sc/fiji/coloc/algorithms/SpearmanRankCorrelation.java
    // (Accessed 2021-08-11)
    HashMap<String, Double> measurements = new HashMap<>();
    // get the 2 images for the calculation of Spearman's rho
    RandomAccessibleInterval<T> img1 = data.getSourceImage1();
    RandomAccessibleInterval<T> img2 = data.getSourceImage2();
    RandomAccessibleInterval<BitType> mask = data.getMask();
    TwinCursor<T> cursor = new TwinCursor<T>(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor());
    // Count the pixels first.
    int n = 0;
    while (cursor.hasNext()) {
        n++;
        cursor.fwd();
    }
    cursor.reset();
    // calculate Spearman's rho value
    SpearmanRankCorrelation src = new SpearmanRankCorrelation<T>();
    double rhoValue = src.calculateSpearmanRank(cursor);
    measurements.put(Measurements.SPEARMAN_RHO, rhoValue);
    measurements.put(Measurements.SPEARMAN_DF, new Double(src.getSpearmanDF(n)).doubleValue());
    measurements.put(Measurements.SPEARMAN_T_STATISTIC, src.getTStatistic(rhoValue, n));
    return measurements;
}

Example 3 with NativeType

use of net.imglib2.type.NativeType in project mia by mianalysis.

the class ManualThreshold method measureManders.

public static <T extends RealType<T> & NativeType<T>> HashMap<String, Double> measureManders(DataContainer<T> data) {
    // Based on code from
    // https://github.com/fiji/Colocalisation_Analysis/blob/master/src/main/java/sc/fiji/coloc/algorithms/MandersColocalization.java
    // (Accessed 2021-08-10)
    HashMap<String, Double> measurements = new HashMap<>();
    MandersColocalization<T> mc = new MandersColocalization<>();
    // get the two images for the calculation of Manders' split coefficients
    RandomAccessible<T> img1 = data.getSourceImage1();
    RandomAccessible<T> img2 = data.getSourceImage2();
    RandomAccessibleInterval<BitType> mask = data.getMask();
    TwinCursor<T> cursor = new TwinCursor<T>(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor());
    // calculate Manders' split coefficients without threshold, M1 and M2.
    MandersResults results = mc.calculateMandersCorrelation(cursor, img1.randomAccess().get().createVariable());
    measurements.put(Measurements.M1_ABOVE_ZERO, results.m1);
    measurements.put(Measurements.M2_ABOVE_ZERO, results.m2);
    // Calculate the thresholded Manders' split coefficients, tM1 and tM2, if
    // possible
    AutoThresholdRegression<T> autoThreshold = data.getAutoThreshold();
    if (autoThreshold != null) {
        // thresholded Manders' split coefficients, tM1 and tM2
        cursor.reset();
        results = mc.calculateMandersCorrelation(cursor, autoThreshold.getCh1MaxThreshold(), autoThreshold.getCh2MaxThreshold(), ThresholdMode.Above);
        measurements.put(Measurements.M1_ABOVE_THRESHOLD, results.m1);
        measurements.put(Measurements.M2_ABOVE_THRESHOLD, results.m2);
    }
    return measurements;
}

Example 4 with NativeType

use of net.imglib2.type.NativeType in project mia by mianalysis.

the class MaskObjects method maskObject.

public static <T extends RealType<T> & NativeType<T>> Obj maskObject(Obj inputObject, Image maskImage) {
    Objs tempObjects = new Objs("Mask objects", inputObject.getObjectCollection());
    // Creating the mask object
    Obj maskObject = tempObjects.createAndAddNewObject(inputObject.getVolumeType(), inputObject.getID());
    maskObject.setT(inputObject.getT());
    ImgPlus<T> maskImg = maskImage.getImgPlus();
    RandomAccess<T> randomAccess = maskImg.randomAccess();
    int xAx = maskImg.dimensionIndex(Axes.X);
    int yAx = maskImg.dimensionIndex(Axes.Y);
    int cAx = maskImg.dimensionIndex(Axes.CHANNEL);
    int zAx = maskImg.dimensionIndex(Axes.Z);
    int tAx = maskImg.dimensionIndex(Axes.TIME);
    // intensity
    for (Point<Integer> point : inputObject.getCoordinateSet()) {
        long[] location = new long[maskImg.numDimensions()];
        if (xAx != -1)
            location[xAx] = point.getX();
        if (yAx != -1)
            location[yAx] = point.getY();
        if (cAx != -1)
            location[cAx] = 0;
        if (zAx != -1)
            location[zAx] = point.getZ();
        if (tAx != -1)
            location[tAx] = inputObject.getT();
        randomAccess.setPosition(location);
        int value = ((UnsignedByteType) randomAccess.get()).get();
        if (value != 0) {
            try {
                maskObject.add(point);
            } catch (PointOutOfRangeException e) {
            }
        }
    }
    return maskObject;
}

Example 5 with NativeType

use of net.imglib2.type.NativeType in project clij2-fft by clij.

the class ImageUtility method cropSymmetric.

public static <T extends ComplexType<T> & NativeType<T>> Img<T> cropSymmetric(RandomAccessibleInterval<T> in, long[] cropSize, OpService ops) {
    long[] min = new long[cropSize.length];
    long[] max = new long[cropSize.length];
    for (int d = 0; d < cropSize.length; d++) {
        min[d] = in.dimension(d) / 2 - cropSize[d] / 2;
        max[d] = min[d] + cropSize[d] - 1;
    }
    Interval interval = new FinalInterval(min, max);
    RandomAccessibleInterval<T> cropped = Views.interval(in, interval);
    Img<T> out = ops.create().img(cropped, Util.getTypeFromInterval(cropped));
    ops.copy().rai(out, cropped);
    return out;
}