Examples with SparseRandomAccessIntType sc.fiji.labkit.ui.utils.sparse.SparseRandomAccessIntType used on opensource projects

Example 1 with SparseRandomAccessIntType

use of sc.fiji.labkit.ui.utils.sparse.SparseRandomAccessIntType in project labkit-ui by juglab.

the class TrainableSegmentationSegmenter method getClassIndices.

private SparseRandomAccessIntType getClassIndices(Labeling labeling, List<String> classes) {
    SparseRandomAccessIntType result = new SparseRandomAccessIntType(labeling, -1);
    Map<Set<Label>, Integer> classIndices = new HashMap<>();
    Function<Set<Label>, Integer> compute = set -> set.stream().mapToInt(label -> classes.indexOf(label.name())).filter(i -> i >= 0).min().orElse(-1);
    Cursor<?> cursor = labeling.sparsityCursor();
    RandomAccess<LabelingType<Label>> randomAccess = labeling.randomAccess();
    RandomAccess<IntType> out = result.randomAccess();
    while (cursor.hasNext()) {
        cursor.fwd();
        randomAccess.setPosition(cursor);
        Set<Label> labels = randomAccess.get();
        if (labels.isEmpty())
            continue;
        Integer classIndex = classIndices.computeIfAbsent(labels, compute);
        out.setPosition(cursor);
        out.get().set(classIndex);
    }
    return result;
}

Example 2 with SparseRandomAccessIntType

use of sc.fiji.labkit.ui.utils.sparse.SparseRandomAccessIntType in project labkit-ui by juglab.

the class MeasureConnectedComponents method connectedComponetsSizes.

static List<Long> connectedComponetsSizes(IterableRegion<BitType> region) {
    List<Long> sizes = new ArrayList<>();
    Cursor<Void> cursor = region.cursor();
    SparseRandomAccessIntType visitedImage = new SparseRandomAccessIntType(region);
    RandomAccess<IntType> visited = visitedImage.randomAccess();
    int currentIndex = 0;
    while (cursor.hasNext()) {
        cursor.fwd();
        visited.setPosition(cursor);
        if (visited.get().get() == 0) {
            currentIndex++;
            long countBefore = visitedImage.sparsityPattern().size();
            Filter<Pair<BitType, IntType>, Pair<BitType, IntType>> filter = (current, seed) -> current.getA().get() && current.getB().get() == 0;
            FloodFill.fill(region, visitedImage, cursor, new IntType(currentIndex), new DiamondShape(1), filter);
            long countAfter = visitedImage.sparsityPattern().size();
            sizes.add(countAfter - countBefore);
        }
    }
    return sizes;
}

Example 3 with SparseRandomAccessIntType

use of sc.fiji.labkit.ui.utils.sparse.SparseRandomAccessIntType in project labkit-ui by juglab.

the class TrainableSegmentationSegmenter method trainFrame.

private void trainFrame(Training training, List<String> classes, Labeling labeling, ImgPlus<?> image, FeatureCalculator featuresCalculator) {
    SparseRandomAccessIntType classIndices = getClassIndices(labeling, classes);
    if (classIndices.sparsityPattern().size() == 0)
        return;
    DiskCachedCellImg<FloatType, ?> cachedFeatureBlock = cachedFeatureBlock(featuresCalculator, image);
    try {
        RandomAccessible<? extends Composite<FloatType>> features = Views.collapse(cachedFeatureBlock);
        addSamples(training, classIndices, features);
    } finally {
        cachedFeatureBlock.shutdown();
    }
}

Example 4 with SparseRandomAccessIntType

use of sc.fiji.labkit.ui.utils.sparse.SparseRandomAccessIntType in project labkit-ui by juglab.

the class Labeling method initImgLabling.

private static ImgLabeling<Label, ?> initImgLabling(Map<Label, IterableRegion<BitType>> regions) {
    Interval interval = getInterval(regions.values());
    ImgLabeling<Label, ?> imgLabeling = new ImgLabeling<>(new SparseRandomAccessIntType(interval));
    RandomAccess<LabelingType<Label>> ra = imgLabeling.randomAccess();
    regions.forEach((label, region) -> {
        Cursor<Void> cursor = region.cursor();
        while (cursor.hasNext()) {
            cursor.fwd();
            ra.setPosition(cursor);
            ra.get().add(label);
        }
    });
    return imgLabeling;
}