Manage SciJava Context lifecycle

And fix failing tests on Windows.

This changes all of labkit-ui to eschew usage of the SingletonContext
class in favor of passing the context between components as appropriate,
creating new contexts in relevant situations, and disposing of contexts
when they are finished being used in all cases except for demo code.

It also escapes backslashes of Windows paths hardcoded into macros,
to account for ImageJ macro using backslash as an escape character.

Some of these changes change existing public API, so this commit
increments the major/minor digit of the development version.

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());