Examples with InputImage sc.fiji.labkit.ui.inputimage.InputImage used on opensource projects

Example 1 with InputImage

use of sc.fiji.labkit.ui.inputimage.InputImage in project labkit-ui by juglab.

the class SegmentationUseCaseTest method test.

@Test
public void test() {
    ImgPlus<UnsignedByteType> image = new ImgPlus<>(ArrayImgs.unsignedBytes(new byte[] { 1, 1, 2, 2 }, 2, 2));
    InputImage inputImage = new DatasetInputImage(image);
    SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(), inputImage);
    addLabels(segmentationModel.imageLabelingModel());
    SegmentationPlugin plugin = PixelClassificationPlugin.create();
    SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(plugin);
    segmenter.train(Collections.singletonList(new ValuePair<>(image, segmentationModel.imageLabelingModel().labeling().get())));
    RandomAccessibleInterval<ShortType> result = segmenter.results(segmentationModel.imageLabelingModel()).segmentation();
    List<Integer> list = new ArrayList<>();
    Views.iterable(result).forEach(x -> list.add(x.getInteger()));
    assertEquals(Arrays.asList(1, 1, 0, 0), list);
}

Example 2 with InputImage

use of sc.fiji.labkit.ui.inputimage.InputImage in project labkit-ui by juglab.

the class LabkitImportPlugin method run.

private static void run(Context context, File file) {
    try {
        ProgressWriter progressWriter = new StatusServiceProgressWriter(context.service(StatusService.class));
        InputImage image = openImage(context, progressWriter, file);
        LabkitFrame.showForImage(context, image);
    } catch (SpimDataInputException e) {
        JOptionPane.showMessageDialog(null, "There was an error when opening: " + file + "\n\n" + e.getMessage(), "Problem", JOptionPane.ERROR_MESSAGE);
    }
}

Example 3 with InputImage

use of sc.fiji.labkit.ui.inputimage.InputImage in project labkit-ui by juglab.

the class ImageLabelingModel method getScaling.

private AffineTransform3D getScaling(Interval inputImage, Interval initialLabeling) {
    long[] dimensionsA = get3dDimensions(inputImage);
    long[] dimensionsB = get3dDimensions(initialLabeling);
    double[] values = IntStream.range(0, 3).mapToDouble(i -> (double) dimensionsA[i] / (double) dimensionsB[i]).toArray();
    AffineTransform3D affineTransform3D = new AffineTransform3D();
    affineTransform3D.set(values[0], 0.0, 0.0, 0.0, 0.0, values[1], 0.0, 0.0, 0.0, 0.0, values[2], 0.0);
    return affineTransform3D;
}