Fix Windows build issues

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>labkit-ui</artifactId>
-	<version>0.4.1-SNAPSHOT</version>
+	<version>0.5.0-SNAPSHOT</version>
 
 	<name>Labkit</name>
 	<description>The Labkit image segmentation tool for Fiji.</description>
@@ -95,6 +95,7 @@
 		<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
 		<bigdataviewer-core.version>10.6.0</bigdataviewer-core.version>
 		<labkit-pixel-classification.version>0.1.18</labkit-pixel-classification.version>
+		<spim_data.version>2.3.4</spim_data.version>
 	</properties>
 
 	<dependencies>

src/main/java/sc/fiji/labkit/ui/LabkitFrame.java

@@ -39,7 +39,6 @@
 import sc.fiji.labkit.ui.models.DefaultSegmentationModel;
 import sc.fiji.labkit.ui.models.SegmentationModel;
 import sc.fiji.labkit.ui.utils.Notifier;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import org.scijava.Context;
 
 import javax.swing.*;
@@ -65,8 +64,6 @@ public class LabkitFrame {
 	public static LabkitFrame showForFile(Context context,
 		final String filename)
 	{
-		if (context == null)
-			context = SingletonContext.getInstance();
 		Dataset dataset = openDataset(context, filename);
 		return showForImage(context, new DatasetInputImage(dataset));
 	}
@@ -83,8 +80,6 @@ private static Dataset openDataset(Context context, String filename) {
 	public static LabkitFrame showForImage(Context context,
 		final InputImage inputImage)
 	{
-		if (context == null)
-			context = SingletonContext.getInstance();
 		final SegmentationModel model = new DefaultSegmentationModel(context, inputImage);
 		model.imageLabelingModel().labeling().set(InitialLabeling.initialLabeling(context, inputImage));
 		return show(model, inputImage.imageForSegmentation().getName());

src/main/java/sc/fiji/labkit/ui/models/DefaultSegmentationModel.java

@@ -92,7 +92,7 @@ List<RandomAccessibleInterval<T>> getSegmentations(T type)
 		Stream<Segmenter> trainedSegmenters = getTrainedSegmenters();
 		return trainedSegmenters
 			.map(segmenter -> {
-				SegmentationTool segmentationTool = new SegmentationTool(segmenter);
+				SegmentationTool segmentationTool = new SegmentationTool(context, segmenter);
 				segmentationTool.setProgressWriter(new DummyProgressWriter());
 				return segmentationTool.segment(image, type);
 			})
@@ -105,7 +105,7 @@ public List<RandomAccessibleInterval<FloatType>> getPredictions() {
 		Stream<Segmenter> trainedSegmenters = getTrainedSegmenters();
 		return trainedSegmenters
 			.map(segmenter -> {
-				SegmentationTool segmentationTool = new SegmentationTool(segmenter);
+				SegmentationTool segmentationTool = new SegmentationTool(context, segmenter);
 				segmentationTool.setProgressWriter(new DummyProgressWriter());
 				return segmentationTool.probabilityMap(image);
 			})

src/main/java/sc/fiji/labkit/ui/panel/AddSegmenterPanel.java

@@ -33,12 +33,13 @@
 import sc.fiji.labkit.ui.models.SegmenterListModel;
 import sc.fiji.labkit.ui.segmentation.SegmentationPlugin;
 import sc.fiji.labkit.ui.segmentation.SegmentationPluginService;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import net.miginfocom.swing.MigLayout;
 import org.scijava.Context;
 
 import javax.swing.*;
 import java.awt.*;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 
 /**
  * Panel that shows a list of available segmentation algorithms. This panel is
@@ -69,10 +70,16 @@ private void addButtons(SegmenterListModel segmenterListModel, JPanel list) {
 
 	public static void main(String... args) {
 		JFrame frame = new JFrame("Select Segmentation Algorithm");
-		Context context = SingletonContext.getInstance();
+		Context context = new Context();
 		SegmenterListModel slm = new SegmenterListModel(context, new ExtensionPoints());
 		frame.add(new AddSegmenterPanel(slm));
 		frame.setSize(300, 300);
 		frame.setVisible(true);
+		frame.addWindowListener(new WindowAdapter() {
+			@Override
+			public void windowClosed(WindowEvent e) {
+				context.dispose();
+			}
+		});
 	}
 }

src/main/java/sc/fiji/labkit/ui/plugin/AbstractProcessFilesInDirectoryPlugin.java

@@ -38,6 +38,7 @@
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.filefilter.WildcardFileFilter;
 import org.scijava.Cancelable;
+import org.scijava.Context;
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
 import org.scijava.log.Logger;
@@ -52,6 +53,9 @@
 
 abstract class AbstractProcessFilesInDirectoryPlugin implements Command, Cancelable {
 
+	@Parameter
+	private Context context;
+
 	@Parameter
 	private DatasetIOService io;
 
@@ -84,7 +88,7 @@ abstract class AbstractProcessFilesInDirectoryPlugin implements Command, Cancela
 
 	@Override
 	public void run() {
-		SegmentationTool segmenter = new SegmentationTool();
+		SegmentationTool segmenter = new SegmentationTool(context);
 		segmenter.setUseGpu(use_gpu);
 		segmenter.openModel(segmenter_file.getAbsolutePath());
 		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));

src/main/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitIJ1Plugin.java

@@ -72,8 +72,7 @@ public class CalculateProbabilityMapWithLabkitIJ1Plugin implements Command, Canc
 
 	@Override
 	public void run() {
-		SegmentationTool segmenter = new SegmentationTool();
-		segmenter.setContext(context);
+		SegmentationTool segmenter = new SegmentationTool(context);
 		segmenter.openModel(segmenter_file.getAbsolutePath());
 		segmenter.setUseGpu(use_gpu);
 		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));

src/main/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitPlugin.java

@@ -74,8 +74,7 @@ public class CalculateProbabilityMapWithLabkitPlugin implements Command, Cancela
 
 	@Override
 	public void run() {
-		SegmentationTool segmenter = new SegmentationTool();
-		segmenter.setContext(context);
+		SegmentationTool segmenter = new SegmentationTool(context);
 		segmenter.openModel(segmenter_file.getAbsolutePath());
 		segmenter.setUseGpu(use_gpu);
 		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));

src/main/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitIJ1Plugin.java

@@ -71,8 +71,7 @@ public class SegmentImageWithLabkitIJ1Plugin implements Command, Cancelable {
 
 	@Override
 	public void run() {
-		SegmentationTool segmenter = new SegmentationTool();
-		segmenter.setContext(context);
+		SegmentationTool segmenter = new SegmentationTool(context);
 		segmenter.setUseGpu(use_gpu);
 		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));
 		segmenter.openModel(segmenter_file.getAbsolutePath());

src/main/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitPlugin.java

@@ -74,8 +74,7 @@ public class SegmentImageWithLabkitPlugin implements Command, Cancelable {
 
 	@Override
 	public void run() {
-		SegmentationTool segmenter = new SegmentationTool();
-		segmenter.setContext(context);
+		SegmentationTool segmenter = new SegmentationTool(context);
 		segmenter.setUseGpu(use_gpu);
 		segmenter.setProgressWriter(new StatusServiceProgressWriter(statusService));
 		segmenter.openModel(segmenter_file.getAbsolutePath());

src/main/java/sc/fiji/labkit/ui/segmentation/SegmentationTool.java

@@ -47,7 +47,6 @@
 import net.imglib2.util.Intervals;
 import org.apache.commons.lang3.ArrayUtils;
 import org.scijava.Context;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import sc.fiji.labkit.ui.inputimage.DatasetInputImage;
 import sc.fiji.labkit.ui.inputimage.ImgPlusViewsOld;
 import sc.fiji.labkit.ui.models.CachedImageFactory;
@@ -71,16 +70,16 @@ public class SegmentationTool {
 
 	private final CachedImageFactory cachedImageFactory = DefaultCachedImageFactory.getInstance();
 
-	public SegmentationTool() {
-
+	public SegmentationTool(Context context) {
+		this(context, null);
 	}
 
-	public SegmentationTool(Segmenter segmenter) {
+	public SegmentationTool(Context context, Segmenter segmenter) {
+		this.context = Objects.requireNonNull(context);
 		this.segmenter = segmenter;
 	}
 
 	public void openModel(String classifierFile) {
-		Context context = this.context != null ? this.context : SingletonContext.getInstance();
 		Segmenter segmenter = new TrainableSegmentationSegmenter(context);
 		segmenter.openModel(classifierFile);
 		setSegmenter(segmenter);
@@ -94,10 +93,6 @@ public void setSegmenter(Segmenter segmenter) {
 			this.segmenter.setUseGpu(useGpu);
 	}
 
-	public void setContext(Context context) {
-		this.context = Objects.requireNonNull(context);
-	}
-
 	public void setProgressWriter(ProgressWriter progressWriter) {
 		this.progressWriter = Objects.requireNonNull(progressWriter);
 	}

src/main/java/sc/fiji/labkit/ui/segmentation/weka/PixelClassificationPlugin.java

@@ -31,7 +31,6 @@
 
 import sc.fiji.labkit.ui.segmentation.SegmentationPlugin;
 import sc.fiji.labkit.ui.segmentation.Segmenter;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import org.scijava.Context;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
@@ -66,8 +65,7 @@ public boolean canOpenFile(String filename) {
 		}
 	}
 
-	public static SegmentationPlugin create() {
-		Context context = SingletonContext.getInstance();
+	public static SegmentationPlugin create(Context context) {
 		PixelClassificationPlugin plugin = new PixelClassificationPlugin();
 		context.inject(plugin);
 		return plugin;

src/test/java/demo/ChangingImageSegmentationComponentDemo.java

@@ -41,7 +41,6 @@
 import sc.fiji.labkit.ui.models.DefaultSegmentationModel;
 import sc.fiji.labkit.ui.models.ImageLabelingModel;
 import sc.fiji.labkit.ui.models.SegmentationModel;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.view.Views;
 import net.miginfocom.swing.MigLayout;
@@ -93,8 +92,7 @@ private static void onChangeImageButtonClicked(SegmentationModel segmentationMod
 		DatasetInputImage datasetInputImage = new DatasetInputImage(image);
 		model.showable().set(datasetInputImage.showable());
 		model.imageForSegmentation().set(datasetInputImage.imageForSegmentation());
-		model.labeling().set(InitialLabeling.initialLabeling(SingletonContext.getInstance(),
-			datasetInputImage));
+		model.labeling().set(InitialLabeling.initialLabeling(new Context(), datasetInputImage));
 	}
 
 	private JPanel getBottomPanel() {

src/test/java/demo/MultiChannelMovieDemo.java

@@ -73,8 +73,12 @@
  */
 public class MultiChannelMovieDemo {
 
+	private static Context context;
+
 	public static void main(String... args) {
+		context = new Context();
 		main2();
+		// TODO: Dispose context when relevant window is closed.
 	}
 
 	private static void main1() {
@@ -120,7 +124,7 @@ public void testInputImageImageForSegmentation() {
 		SegmentationModel segmentationModel = new DefaultSegmentationModel(
 			new Context(), inputImage);
 		SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(
-			PixelClassificationPlugin.create());
+			PixelClassificationPlugin.create(context));
 		Labeling labeling1 = labeling5d();
 		segmentationModel.imageLabelingModel().labeling().set(labeling1);
 		segmenter.train(Collections.singletonList(new ValuePair<>(inputImage

src/test/java/sc/fiji/labkit/ui/InitialLabelingTest.java

@@ -34,7 +34,9 @@
 import net.imagej.axis.EnumeratedAxis;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;
-import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.scijava.Context;
 import sc.fiji.labkit.ui.inputimage.DatasetInputImage;
 import sc.fiji.labkit.ui.labeling.Labeling;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
@@ -49,6 +51,18 @@
 
 public class InitialLabelingTest {
 
+	private static Context context;
+
+	@BeforeClass
+	public static void setUp() {
+		context = new Context();
+	}
+
+	@AfterClass
+	public static void tearDown() {
+		context.dispose();
+	}
+
 	@Test
 	public void testDoNotCrashWhenLabelingFileIsEmpty() throws IOException {
 		File empty = File.createTempFile("labkit-InitialLabelingTest-",
@@ -59,7 +73,7 @@ public void testDoNotCrashWhenLabelingFileIsEmpty() throws IOException {
 			DatasetInputImage inputImage = new DatasetInputImage(image);
 			List<String> defaultLabels = Collections.emptyList();
 			Labeling result = InitialLabeling.initLabeling(inputImage,
-				SingletonContext.getInstance(),
+				context,
 				defaultLabels);
 			assertNotNull(result);
 		}
@@ -75,7 +89,7 @@ public void testEnumeratedAxis() {
 		EnumeratedAxis yAxis = new EnumeratedAxis(Axes.Y, "mm", new double[] { 0, 0.3 });
 		ImgPlus<UnsignedByteType> image = new ImgPlus<>(img, "test", xAxis, yAxis);
 		DatasetInputImage inputImage = new DatasetInputImage(image);
-		Labeling result = InitialLabeling.initialLabeling(SingletonContext.getInstance(), inputImage);
+		Labeling result = InitialLabeling.initialLabeling(context, inputImage);
 		assertNotNull(result);
 	}
 }

src/test/java/sc/fiji/labkit/ui/SegmentationUseCaseTest.java

@@ -39,6 +39,8 @@
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.type.numeric.IntegerType;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 import sc.fiji.labkit.ui.bdv.BdvShowable;
 import sc.fiji.labkit.ui.inputimage.DatasetInputImage;
 import sc.fiji.labkit.ui.inputimage.InputImage;
@@ -51,7 +53,6 @@
 import sc.fiji.labkit.ui.segmentation.weka.PixelClassificationPlugin;
 import sc.fiji.labkit.ui.segmentation.SegmentationPlugin;
 import net.imglib2.roi.labeling.LabelingType;
-import net.imglib2.type.numeric.integer.ShortType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.util.Intervals;
 import net.imglib2.util.ValuePair;
@@ -70,22 +71,34 @@
 
 public class SegmentationUseCaseTest {
 
+	private static Context context;
+
+	@BeforeClass
+	public static void setUp() {
+		context = new Context();
+	}
+
+	@AfterClass
+	public static void tearDown() {
+		context.dispose();
+	}
+
 	@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);
+			context, inputImage);
 		addLabels(segmentationModel.imageLabelingModel());
-		SegmentationPlugin plugin = PixelClassificationPlugin.create();
+		SegmentationPlugin plugin = PixelClassificationPlugin.create(context);
 		SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(plugin);
 		segmenter.train(Collections.singletonList(new ValuePair<>(image,
 			segmentationModel.imageLabelingModel().labeling().get())));
 		RandomAccessibleInterval<? extends IntegerType<?>> result =
 			segmenter.results(segmentationModel.imageLabelingModel()).segmentation();
 		List<Integer> list = new ArrayList<>();
-		Views.iterable(result).forEach(x -> list.add(x.getInteger()));
+		result.forEach(x -> list.add(x.getInteger()));
 		assertEquals(Arrays.asList(1, 1, 0, 0), list);
 	}
 
@@ -99,7 +112,7 @@ private void addLabels(ImageLabelingModel imageLabelingModel) {
 	}
 
 	@Test
-	public void testMultiChannel() throws InterruptedException {
+	public void testMultiChannel() {
 		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",
@@ -108,17 +121,17 @@ public void testMultiChannel() throws InterruptedException {
 			.wrap(Views.hyperSlice(img, 2, 0)));
 
 		Labeling labeling = getLabeling();
-		SegmentationModel segmentationModel = new DefaultSegmentationModel(new Context(),
+		SegmentationModel segmentationModel = new DefaultSegmentationModel(context,
 			inputImage);
 		ImageLabelingModel imageLabelingModel = segmentationModel.imageLabelingModel();
 		imageLabelingModel.labeling().set(labeling);
 		SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(
-			PixelClassificationPlugin.create());
+			PixelClassificationPlugin.create(context));
 		segmenter.train(Collections.singletonList(new ValuePair<>(imgPlus,
 			imageLabelingModel.labeling().get())));
 		RandomAccessibleInterval<? extends IntegerType<?>> result =
 			segmenter.results(imageLabelingModel).segmentation();
-		Iterator<? extends IntegerType<?>> it = Views.iterable(result).iterator();
+		Iterator<? extends IntegerType<?>> it = result.iterator();
 		assertEquals(1, it.next().getInteger());
 		assertEquals(0, it.next().getInteger());
 		assertEquals(0, it.next().getInteger());