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

Example 1 with DatasetInputImage

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

the class ChangingImageSegmentationComponentDemo method onChangeImageButtonClicked.

private static void onChangeImageButtonClicked(SegmentationModel segmentationModel) {
    final ImagePlus imp = new ImagePlus("https://imagej.nih.gov/ij/images/apple.tif");
    ImageLabelingModel model = segmentationModel.imageLabelingModel();
    ImgPlus<?> image = VirtualStackAdapter.wrap(imp);
    DatasetInputImage datasetInputImage = new DatasetInputImage(image);
    model.showable().set(datasetInputImage.showable());
    model.imageForSegmentation().set(datasetInputImage.imageForSegmentation());
    model.labeling().set(InitialLabeling.initialLabeling(SingletonContext.getInstance(), datasetInputImage));
}

Example 2 with DatasetInputImage

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

the class LabelingComponentDemo method initModel.

private static ImageLabelingModel initModel() {
    final ImagePlus imp = new ImagePlus("https://imagej.nih.gov/ij/images/FluorescentCells.jpg");
    ImgPlus<?> image = VirtualStackAdapter.wrap(imp);
    return new ImageLabelingModel(new DatasetInputImage(image));
}

Example 3 with DatasetInputImage

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

the class MultiChannelMovieDemo method testInputImageImageForSegmentation.

@Test
public void testInputImageImageForSegmentation() {
    DatasetInputImage inputImage = inputImage5d();
    SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(), inputImage);
    SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(PixelClassificationPlugin.create());
    Labeling labeling1 = labeling5d();
    segmentationModel.imageLabelingModel().labeling().set(labeling1);
    segmenter.train(Collections.singletonList(new ValuePair<>(inputImage.imageForSegmentation(), labeling1)));
    RandomAccessibleInterval<ShortType> result = segmenter.results(segmentationModel.imageLabelingModel()).segmentation();
    Labeling labeling = labeling5d();
    LoopBuilder.setImages(labeling, result).forEachPixel((l, r) -> {
        if (l.contains("foreground"))
            assertEquals(1, r.get());
        if (l.contains("background"))
            assertEquals(0, r.get());
    });
}

Example 4 with DatasetInputImage

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

the class MultiChannelMovieDemo method main2.

private static void main2() {
    DatasetInputImage inputImage = inputImage5d();
    LabkitFrame.showForImage(new Context(), inputImage);
}

Example 5 with DatasetInputImage

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

the class SegmentationUseCaseTest method testMultiChannel.

@Test
public void testMultiChannel() throws InterruptedException {
    Img<UnsignedByteType> img = ArrayImgs.unsignedBytes(new byte[] { -1, 0, -1, 0, -1, -1, 0, 0 }, 2, 2, 2);
    ImgPlus<UnsignedByteType> imgPlus = new ImgPlus<>(img, "Image", new AxisType[] { Axes.X, Axes.Y, Axes.CHANNEL });
    DatasetInputImage inputImage = new DatasetInputImage(imgPlus, BdvShowable.wrap(Views.hyperSlice(img, 2, 0)));
    Labeling labeling = getLabeling();
    SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(), inputImage);
    ImageLabelingModel imageLabelingModel = segmentationModel.imageLabelingModel();
    imageLabelingModel.labeling().set(labeling);
    SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(PixelClassificationPlugin.create());
    segmenter.train(Collections.singletonList(new ValuePair<>(imgPlus, imageLabelingModel.labeling().get())));
    RandomAccessibleInterval<ShortType> result = segmenter.results(imageLabelingModel).segmentation();
    Iterator<ShortType> it = Views.iterable(result).iterator();
    assertEquals(1, it.next().get());
    assertEquals(0, it.next().get());
    assertEquals(0, it.next().get());
    assertEquals(0, it.next().get());
    assertTrue(Intervals.equals(new FinalInterval(2, 2), result));
}