Examples with Interval net.imglib2.Interval used on opensource projects

Example 6 with Interval

use of net.imglib2.Interval in project vcell by virtualcell.

the class ImageStatsForPlotting method computeMean.

/**
 * Computes the mean of each XY slice along the 3rd dimension
 * TODO: Currently assumes only 3 dimensions, must handle time series of z stacks and multiple channels
 * @param data
 * @return Pair containing A) the 3rd dimension index, and B) the mean value of the XY slice
 */
private Pair<double[], double[]> computeMean(RandomAccessibleInterval<T> data, IterableInterval<BitType> mask) {
    double[] indices = new double[(int) data.dimension(2)];
    double[] means = new double[indices.length];
    for (int z = 0; z < indices.length; z++) {
        FinalInterval interval = Intervals.createMinMax(0, 0, z, data.dimension(0) - 1, data.dimension(1) - 1, z);
        double mean = 0.0;
        RandomAccessibleInterval<T> cropped = ops.transform().crop(data, interval);
        if (mask == null) {
            mean = ops.stats().mean(Views.iterable(cropped)).getRealDouble();
        } else {
            Cursor<BitType> maskCursor = mask.localizingCursor();
            RandomAccess<T> dataRA = cropped.randomAccess();
            RealSum sum = new RealSum();
            int size = 0;
            maskCursor.reset();
            while (maskCursor.hasNext()) {
                maskCursor.fwd();
                if (maskCursor.get().get()) {
                    dataRA.setPosition(maskCursor);
                    sum.add(dataRA.get().getRealDouble());
                    size++;
                }
            }
            mean = sum.getSum() / size;
        }
        indices[z] = z;
        means[z] = mean;
    }
    return new ValuePair<double[], double[]>(indices, means);
}

Example 7 with Interval

use of net.imglib2.Interval in project vcell by virtualcell.

the class LargestRegionSlice method run.

@Override
public void run() {
    int maxArea = 0;
    int zOfMaxArea = 0;
    for (int z = 0; z < data.dimension(2); z++) {
        FinalInterval interval = Intervals.createMinMax(0, 0, z, data.dimension(0) - 1, data.dimension(1) - 1, z);
        RandomAccessibleInterval<BitType> croppedRAI = ops.transform().crop(data, interval);
        IterableInterval<BitType> croppedII = Views.iterable(croppedRAI);
        Cursor<BitType> cursor = croppedII.cursor();
        int area = 0;
        while (cursor.hasNext()) {
            if (cursor.next().get()) {
                area++;
            }
        }
        if (area > maxArea) {
            maxArea = area;
            zOfMaxArea = z;
        }
    }
    FinalInterval interval = Intervals.createMinMax(0, 0, zOfMaxArea, data.dimension(0) - 1, data.dimension(1) - 1, zOfMaxArea);
    output = ops.transform().crop(data, interval);
}