Examples with Segmenter sc.fiji.labkit.ui.segmentation.Segmenter used on opensource projects

Example 1 with Segmenter

use of sc.fiji.labkit.ui.segmentation.Segmenter in project labkit-ui by juglab.

the class TrainableSegmentationSegmenter method train.

@Override
public void train(List<Pair<ImgPlus<?>, Labeling>> trainingData) {
    try {
        initFeatureSettings(trainingData);
        List<String> classes = collectLabels(trainingData.stream().map(Pair::getB).collect(Collectors.toList()));
        sc.fiji.labkit.pixel_classification.classification.Segmenter segmenter = new sc.fiji.labkit.pixel_classification.classification.Segmenter(context, classes, featureSettings, new FastRandomForest());
        segmenter.setUseGpu(useGpu);
        Training training = segmenter.training();
        for (Pair<ImgPlus<?>, Labeling> pair : trainingData) trainStack(training, classes, pair.getB(), pair.getA(), segmenter.features());
        training.train();
        this.segmenter = segmenter;
    } catch (RuntimeException e) {
        Throwable cause = e.getCause();
        if (cause instanceof WekaException && cause.getMessage().contains("Not enough training instances"))
            throw new CancellationException("The training requires some labeled regions.");
        throw e;
    }
}

Example 2 with Segmenter

use of sc.fiji.labkit.ui.segmentation.Segmenter in project labkit-ui by juglab.

the class DefaultSegmentationModel method getPredictions.

public List<RandomAccessibleInterval<FloatType>> getPredictions() {
    ImgPlus<?> image = imageLabelingModel().imageForSegmentation().get();
    Stream<Segmenter> trainedSegmenters = getTrainedSegmenters();
    return trainedSegmenters.map(segmenter -> {
        int numberOfClasses = segmenter.classNames().size();
        RandomAccessibleInterval<FloatType> prediction = new CellImgFactory<>(new FloatType()).create(DimensionUtils.appendDimensionToInterval(image, 0, numberOfClasses - 1));
        segmenter.predict(image, prediction);
        return prediction;
    }).collect(Collectors.toList());
}