Examples with Label sc.fiji.labkit.ui.labeling.Label used on opensource projects

Example 1 with Label

use of sc.fiji.labkit.ui.labeling.Label 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 Label

use of sc.fiji.labkit.ui.labeling.Label in project labkit-ui by juglab.

the class CustomSegmenter method train.

/**
 * Calculates the mean intensity value for all foreground pixel, and the mean
 * intensity value for all background pixel.
 */
@Override
public void train(List<Pair<ImgPlus<?>, Labeling>> data) {
    MeanCalculator foregroundMean = new MeanCalculator();
    MeanCalculator backgroundMean = new MeanCalculator();
    for (Pair<ImgPlus<?>, Labeling> imageAndLabeling : data) {
        RandomAccessibleInterval<? extends RealType<?>> image = grayScale(imageAndLabeling.getA());
        Labeling labeling = imageAndLabeling.getB();
        Map<Label, IterableRegion<BitType>> regions = labeling.iterableRegions();
        for (Label label : regions.keySet()) {
            String name = label.name();
            IterableRegion<BitType> region = regions.get(label);
            switch(name) {
                case "foreground":
                    foregroundMean.addSample(image, region);
                    break;
                case "background":
                    backgroundMean.addSample(image, region);
                    break;
                default:
                    throw new RuntimeException("Unsupported label name \"" + name + "\"\n" + "Threshold expects the labels to be named \"foreground\" and \"background\".");
            }
        }
    }
    this.foreground = foregroundMean.mean();
    this.background = backgroundMean.mean();
}

Example 3 with Label

use of sc.fiji.labkit.ui.labeling.Label in project labkit-ui by juglab.

the class DefaultSegmentationModelTest method testLoadClassifierWithDifferentLabels.

@Test
public void testLoadClassifierWithDifferentLabels() throws IOException {
    // This test reproduced a NoSuchElementException, that appeared when
    // a classifier is loaded, that was trained on a label, whose name
    // doesn't appear in the current labeling.
    // create model
    DatasetInputImage image = new DatasetInputImage(ArrayImgs.unsignedBytes(1, 1));
    SegmentationModel model = new DefaultSegmentationModel(new Context(), image);
    // train classifier
    Labeling labeling = model.imageLabelingModel().labeling().get();
    List<Label> labels = labeling.getLabels();
    Views.iterable(labeling.getRegion(labels.get(0))).forEach(BitType::setOne);
    SegmentationItem item = model.segmenterList().addSegmenter(PixelClassificationPlugin.create());
    item.train(Collections.singletonList(new ValuePair<>(image.imageForSegmentation(), labeling)));
    // save classifier
    File tmpFile = File.createTempFile("model", ".classifier");
    tmpFile.deleteOnExit();
    item.saveModel(tmpFile.getAbsolutePath());
    // remove labels
    for (Label label : labels) labeling.removeLabel(label);
    // open classifier
    item.openModel(tmpFile.getAbsolutePath());
}

Example 4 with Label

use of sc.fiji.labkit.ui.labeling.Label in project labkit-ui by juglab.

the class BitmapImportExportAction method exportLabel.

private void exportLabel(Void ignore, String filename) throws IOException {
    Label label = model.selectedLabel().get();
    exportLabel(label, filename);
}

Example 5 with Label

use of sc.fiji.labkit.ui.labeling.Label in project labkit-ui by juglab.

the class SegmentationAsLabelAction method addLabel.

// TODO move to better place
private static void addLabel(Labeling labeling, String name, RandomAccessibleInterval<BitType> mask) {
    Cursor<BitType> cursor = Views.iterable(mask).cursor();
    Label label = labeling.addLabel(name);
    RandomAccess<LabelingType<Label>> ra = labeling.randomAccess();
    while (cursor.hasNext()) {
        boolean value = cursor.next().get();
        if (value) {
            ra.setPosition(cursor);
            ra.get().add(label);
        }
    }
}