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

Example 6 with Labeling

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

the class FloodFillTest method test2.

@Test
public void test2() {
    RandomAccessibleInterval<LabelingType<String>> labeling = exampleImgLabeling();
    Predicate<LabelingType<String>> visit = set -> set.contains("a") && set.contains("b") && !set.contains("ab");
    final Point seed = new Point(2, 2);
    FloodFill.cachedFloodFill(labeling, seed, visit, l -> l.add("ab"));
    assertLabelEqualsInterval(labeling, intervalA, "a");
    assertLabelEqualsInterval(labeling, intervalB, "b");
    assertLabelEqualsInterval(labeling, intervalC, "c");
    assertLabelEqualsInterval(labeling, intervalAintersectB, "ab");
}

Example 7 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling 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 8 with Labeling

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

the class InitialLabelingTest method testInitialLabeling.

@Test
public void testInitialLabeling() throws IOException {
    File empty = File.createTempFile("labkit-InitialLabelingTest-", ".czi.labeling");
    try {
        ImgPlus<UnsignedByteType> image = ImgPlus.wrap(ArrayImgs.unsignedBytes(2, 3));
        image.setSource(empty.getAbsolutePath().replace(".labeling", ""));
        DatasetInputImage inputImage = new DatasetInputImage(image);
        Context context = new Context();
        List<String> defaultLabels = Collections.emptyList();
        Labeling result = InitialLabeling.initLabeling(inputImage, context, defaultLabels);
        assertNotNull(result);
    } finally {
        empty.delete();
    }
}

Example 9 with Labeling

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

the class TrainableSegmentationSegmenterTest method testClassify3DStackInSlices.

@Test
public void testClassify3DStackInSlices() {
    Context context = SingletonContext.getInstance();
    TrainableSegmentationSegmenter segmenter = new TrainableSegmentationSegmenter(context);
    // Settings to 2D
    segmenter.setFeatureSettings(new FeatureSettings(GlobalSettings.default2d().build(), SingleFeatures.identity()));
    // Train on 3D image
    ImgPlus<?> image3d = new ImgPlus<>(ArrayImgs.ints(new int[] { 0, 1, 1, 0 }, 2, 1, 2), "name", new AxisType[] { Axes.X, Axes.Y, Axes.Z });
    Labeling labeling = initLabeling();
    segmenter.train(Collections.singletonList(new ValuePair<>(image3d, labeling)));
    // Segment 3D image
    Img<IntType> result = ArrayImgs.ints(2, 1, 2);
    segmenter.segment(image3d, result);
    ImgLib2Assert.assertImageEquals(image3d, result, Object::equals);
    Img<IntType> expected2d = ArrayImgs.ints(new int[] { 0, 1, 0 }, 1, 3);
    // Segment 2d image
    ImgPlus<IntType> image2d = new ImgPlus<>(expected2d, "");
    Img<IntType> result2d = ArrayImgs.ints(1, 3);
    segmenter.segment(image2d, result2d);
    ImgLib2Assert.assertImageEquals(image2d, result2d, Object::equals);
}

Example 10 with Labeling

use of sc.fiji.labkit.ui.labeling.Labeling 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());
}