Adds simple labkit plugin

src/main/java/net/imglib2/labkit/labeling/LabelingSerializer.java

@@ -153,7 +153,7 @@ private <I extends IntegerType<I>> void saveAsTiff(Labeling labeling,
 		io.save(ds.create(imgPlus), filename);
 	}
 
-	private static class LabelsMetaData {
+	public static class LabelsMetaData {
 
 		List<Set<String>> labelSets;
 

src/main/java/net/imglib2/labkit/models/DefaultSegmentationModel.java

@@ -127,10 +127,10 @@ public SegmentationItem addSegmenter() {
 
 	@Override
 	public void train(SegmentationItem item) {
-		ParallelUtils.runInOtherThread(() -> internTrain(item));
+		ParallelUtils.runInOtherThread(() -> trainAndWait(item));
 	}
 
-	private void internTrain(SegmentationItem item) {
+	public void trainAndWait(SegmentationItem item) {
 		SwingProgressWriter progressWriter = new SwingProgressWriter(null,
 			"Training in Progress");
 		progressWriter.setVisible(true);

src/main/java/net/imglib2/labkit/plugin/SimpleLabkitPlugin.java

@@ -0,0 +1,83 @@
+package net.imglib2.labkit.plugin;
+
+import ij.ImagePlus;
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.labkit.BatchSegmenter;
+import net.imglib2.labkit.inputimage.DefaultInputImage;
+import net.imglib2.labkit.labeling.Labeling;
+import net.imglib2.labkit.labeling.LabelingSerializer;
+import net.imglib2.labkit.models.DefaultSegmentationModel;
+import net.imglib2.labkit.models.ImageLabelingModel;
+import net.imglib2.labkit.utils.progress.StatusServiceProgressWriter;
+import net.imglib2.roi.labeling.ImgLabeling;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.IntegerType;
+import net.imglib2.util.Intervals;
+import org.scijava.Context;
+import org.scijava.ItemIO;
+import org.scijava.app.StatusService;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import static net.imglib2.labkit.labeling.LabelingSerializer.fromImageAndLabelSets;
+
+@Plugin( type = Command.class, menuPath = "Plugins>Segmentation>Label (simple mode)" )
+public class SimpleLabkitPlugin implements Command {
+
+	@Parameter
+	Img input;
+
+	@Parameter
+	Img<? extends IntegerType<?>> labeling;
+
+	@Parameter(type = ItemIO.OUTPUT)
+	Img output;
+
+	@Parameter
+	Context context;
+
+	@Parameter
+	StatusService statusService;
+
+	@Override
+	public void run() {
+
+		// init segmentation model, serializer, labeling model
+		DefaultSegmentationModel segmentationModel = new DefaultSegmentationModel( new DefaultInputImage(
+				input ), context );
+		final ImageLabelingModel labelingModel = segmentationModel
+				.imageLabelingModel();
+
+		// load labeling from labeling img
+		LabelingSerializer.LabelsMetaData meta = new LabelingSerializer.LabelsMetaData(labeling);
+		ImgLabeling<String, ?> imgLabeling = fromImageAndLabelSets(labeling, meta.asLabelSets());
+		labelingModel.labeling().set( Labeling.fromImgLabeling(imgLabeling) );
+		if ( labelingModel.labeling().get().getLabels().size() == 0 )
+		{
+			System.out.println( "no labels" );
+			return;
+		}
+
+		// train
+		segmentationModel.trainAndWait( segmentationModel
+				.selectedSegmenter().get() );
+
+		// run segmentation
+		final ImagePlus segImgImagePlus = ImageJFunctions.wrap( input, "seginput" );
+		final Img<ARGBType> segImg = ImageJFunctions.wrap(segImgImagePlus);
+		try
+		{
+			output = BatchSegmenter.segment( segImg,
+					segmentationModel.selectedSegmenter().get(),
+					Intervals.dimensionsAsIntArray( segImg ),
+					new StatusServiceProgressWriter( statusService ) );
+		}
+		catch ( InterruptedException e )
+		{
+			e.printStackTrace();
+		}
+
+	}
+}

src/test/java/net/imglib2/labkit/plugin/SimpleLabkitPluginDemo.java

@@ -0,0 +1,74 @@
+package net.imglib2.labkit.plugin;
+
+import net.imagej.ImageJ;
+import net.imglib2.RandomAccess;
+import net.imglib2.img.Img;
+import net.imglib2.type.numeric.integer.ByteType;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.real.DoubleType;
+import org.junit.Test;
+import org.scijava.command.CommandModule;
+
+import java.util.concurrent.ExecutionException;
+
+import static org.junit.Assert.assertEquals;
+
+public class SimpleLabkitPluginDemo {
+
+	@Test
+	public void run() throws ExecutionException, InterruptedException {
+		ImageJ ij = new ImageJ();
+
+		long[] dims = new long[]{10,10};
+
+		//create input image, set values to zero, left top quarter to one
+		Img<DoubleType> input = ij.op().create().img(dims);
+		RandomAccess<DoubleType> inputRA = input.randomAccess();
+		for (int i = 0; i < dims[0]; i++) {
+			for (int j = 0; j < dims[1]; j++) {
+				inputRA.setPosition(new int[]{i,j});
+				if(i < 5 && j < 5) {
+					inputRA.get().setOne();
+				} else {
+					inputRA.get().setZero();
+				}
+			}
+		}
+
+		//create labeling with first pixel labeled one, rest zero
+		Img<ByteType> labeling = ij.op().convert().int8(ij.op().create().img(dims));
+		labeling.forEach(pixel -> pixel.setZero());
+		labeling.firstElement().setReal(2.0);
+		RandomAccess<ByteType> labelingRA = labeling.randomAccess();
+		labelingRA.setPosition(new int[]{(int) (dims[0]-1), (int) (dims[1]-1)});
+		labelingRA.get().setOne();
+
+		ij.ui().show(input);
+		ij.ui().show(labeling);
+
+		// run labkit command
+		CommandModule result = ij.command().run(SimpleLabkitPlugin.class, true, "input", input, "labeling", labeling).get();
+		Img output = (Img) result.getOutput("output");
+
+		ij.ui().show("output", output);
+		// result control
+		assertEquals(dims[0], output.dimension(0));
+		assertEquals(dims[1], output.dimension(1));
+		RandomAccess<UnsignedByteType> outputRA = output.randomAccess();
+		for (int i = 0; i < dims[0]; i++) {
+			for (int j = 0; j < dims[1]; j++) {
+				outputRA.setPosition(new int[]{i,j});
+				if(i < 5 && j < 5) {
+					assertEquals(1, outputRA.get().get());
+				}else {
+					assertEquals(0, outputRA.get().get());
+				}
+			}
+		}
+	}
+
+	public static void main(String... args) throws ExecutionException, InterruptedException {
+		new SimpleLabkitPluginDemo().run();
+	}
+
+}