Merge pull request #115, update to imglib2-7.1

Addition of getType() API

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>34.1.0</version>
+		<version>38.0.1</version>
 	</parent>
 
 	<groupId>sc.fiji</groupId>
@@ -85,24 +85,16 @@
 		<license.licenseName>bsd_2</license.licenseName>
 		<license.copyrightOwners>Matthias Arzt</license.copyrightOwners>
 
-		<imglib2.version>6.1.0</imglib2.version>
-		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
-		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
-		<bigdataviewer-vistools.version>1.0.0-beta-32</bigdataviewer-vistools.version>
-
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
-		<imagej-deprecated.version>0.2.0</imagej-deprecated.version>
-		<imagej-ops.version>2.0.0</imagej-ops.version>
-		<imglib2.version>6.1.0</imglib2.version>
-		<imglib2-algorithm.version>0.13.2</imglib2-algorithm.version>
-		<imglib2-algorithm-gpl.version>0.3.1</imglib2-algorithm-gpl.version>
-		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
-		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
-		<imglib2-roi.version>0.14.0</imglib2-roi.version>
-		<scifio.version>0.45.0</scifio.version>
+		<imglib2.version>7.1.0</imglib2.version>
+		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
+		<imglib2-roi.version>0.15.0</imglib2-roi.version>
+		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
+		<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>
 	</properties>
 
 	<dependencies>
@@ -198,10 +190,6 @@
 			<groupId>sc.fiji</groupId>
 			<artifactId>bigdataviewer-core</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>sc.fiji</groupId>
-			<artifactId>bigdataviewer-vistools</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-realtransform</artifactId>

src/main/java/sc/fiji/labkit/ui/actions/AddLabelingIoAction.java

@@ -84,7 +84,7 @@ private void addLabel(Labeling labeling, Label label,
 			.stream().map(Label::name).collect(Collectors.toList()));
 		if (newLabelName == null) return;
 		Label newLabel = labeling.addLabel(newLabelName);
-		Cursor<Void> cursor = region.cursor();
+		Cursor<Void> cursor = region.inside().cursor();
 		RandomAccess<LabelingType<Label>> ra = labeling.randomAccess();
 		while (cursor.hasNext()) {
 			cursor.fwd();

src/main/java/sc/fiji/labkit/ui/brush/LabelBrushController.java

@@ -40,6 +40,7 @@
 import net.imglib2.roi.IterableRegion;
 import net.imglib2.roi.Regions;
 import net.imglib2.type.logic.BitType;
+import net.imglib2.util.Intervals;
 import org.scijava.ui.behaviour.*;
 import sc.fiji.labkit.ui.ActionsAndBehaviours;
 import sc.fiji.labkit.ui.brush.neighborhood.Ellipsoid;
@@ -248,8 +249,8 @@ private List<Label> getVisibleLabels() {
 		private RandomAccessible<LabelingType<Label>> extendLabelingType(
 			RandomAccessibleInterval<LabelingType<Label>> slice)
 		{
-			LabelingType<Label> variable = Util.getTypeFromInterval(slice)
-				.createVariable();
+			LabelingType<Label> variable = slice.randomAccess()
+				.setPositionAndGet(Intervals.minAsLongArray(slice)).createVariable();
 			variable.clear();
 			return Views.extendValue(slice, variable);
 		}

src/main/java/sc/fiji/labkit/ui/labeling/Labeling.java

@@ -142,7 +142,7 @@ public static Labeling fromMap(Map<String, IterableRegion<BitType>> regions) {
 			new SparseRandomAccessIntType(interval));
 		RandomAccess<LabelingType<Label>> ra = imgLabeling.randomAccess();
 		regions.forEach((label, region) -> {
-			Cursor<Void> cursor = region.cursor();
+			Cursor<Void> cursor = region.inside().cursor();
 			while (cursor.hasNext()) {
 				cursor.fwd();
 				ra.setPosition(cursor);
@@ -303,6 +303,12 @@ public void setLabelOrder(Comparator<? super Label> comparator) {
 		labels.sort(comparator);
 	}
 
+	@Override
+	public LabelingType< Label > getType()
+	{
+		return randomAccess().getType();
+	}
+
 	public static class SetEntryAsBitType<T> extends BitType {
 
 		private Set<T> set = null;

src/main/java/sc/fiji/labkit/ui/labeling/LabelingSerializer.java

@@ -266,7 +266,7 @@ private JsonElement regionToJson(Gson gson,
 			IterableRegion<BitType> region)
 		{
 			JsonArray result = new JsonArray();
-			Cursor<Void> cursor = region.cursor();
+			Cursor<Void> cursor = region.inside().cursor();
 			long[] coords = new long[cursor.numDimensions()];
 			while (cursor.hasNext()) {
 				cursor.fwd();

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

@@ -141,7 +141,7 @@ public void localizeLabel(final Label label) {
 
 	private static Interval getBoundingBox(IterableRegion<BitType> region) {
 		int numDimensions = region.numDimensions();
-		Cursor<?> cursor = region.cursor();
+		Cursor<?> cursor = region.inside().cursor();
 		if (!cursor.hasNext()) return null;
 		long[] min = new long[numDimensions];
 		long[] max = new long[numDimensions];

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

@@ -114,7 +114,7 @@ public static void addAction(Extensible extensible, LabelingModel model) {
 
 	static List<Long> connectedComponetsSizes(IterableRegion<BitType> region) {
 		List<Long> sizes = new ArrayList<>();
-		Cursor<Void> cursor = region.cursor();
+		Cursor<Void> cursor = region.inside().cursor();
 		SparseRandomAccessIntType visitedImage = new SparseRandomAccessIntType(
 			region);
 		RandomAccess<IntType> visited = visitedImage.randomAccess();
@@ -124,12 +124,12 @@ static List<Long> connectedComponetsSizes(IterableRegion<BitType> region) {
 			visited.setPosition(cursor);
 			if (visited.get().get() == 0) {
 				currentIndex++;
-				long countBefore = visitedImage.sparsityPattern().size();
+				long countBefore = visitedImage.sparsityPattern().inside().size();
 				Filter<Pair<BitType, IntType>, Pair<BitType, IntType>> filter = (
 					current, seed) -> current.getA().get() && current.getB().get() == 0;
 				FloodFill.fill(region, visitedImage, cursor, new IntType(currentIndex),
 					new DiamondShape(1), filter);
-				long countAfter = visitedImage.sparsityPattern().size();
+				long countAfter = visitedImage.sparsityPattern().inside().size();
 				sizes.add(countAfter - countBefore);
 			}
 		}

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

@@ -260,7 +260,7 @@ private void trainFrame(Training training, List<String> classes, Labeling labeli
 		ImgPlus<?> image, FeatureCalculator featuresCalculator)
 	{
 		SparseRandomAccessIntType classIndices = getClassIndices(labeling, classes);
-		if (classIndices.sparsityPattern().size() == 0)
+		if (classIndices.sparsityPattern().inside().size() == 0)
 			return;
 		DiskCachedCellImg<FloatType, ?> cachedFeatureBlock = cachedFeatureBlock(featuresCalculator,
 			image);

src/main/java/sc/fiji/labkit/ui/utils/sparse/SparseIterableRegion.java

@@ -35,6 +35,7 @@
 import net.imglib2.AbstractWrappedInterval;
 import net.imglib2.Cursor;
 import net.imglib2.Interval;
+import net.imglib2.IterableInterval;
 import net.imglib2.Localizable;
 import net.imglib2.Point;
 import net.imglib2.RandomAccess;
@@ -56,6 +57,8 @@ public class SparseIterableRegion extends AbstractWrappedInterval<Interval>
 
 	final private IntervalIndexer2 indexer;
 
+	private final InsideIterable inside;
+
 	public SparseIterableRegion(Interval interval) {
 		this(interval, new TLongHashSet());
 	}
@@ -64,6 +67,7 @@ public SparseIterableRegion(Interval interval, TLongSet positions) {
 		super(interval);
 		this.codes = positions;
 		this.indexer = new IntervalIndexer2(interval);
+		this.inside = new InsideIterable();
 	}
 
 	public void add(Localizable position) {
@@ -79,43 +83,58 @@ private boolean contains(Localizable position) {
 	}
 
 	@Override
-	public Cursor<Void> cursor() {
-		return new SparseRoiCursor();
+	public RandomAccess<BitType> randomAccess() {
+		return new SparseRoiRandomAccess();
 	}
 
 	@Override
-	public Cursor<Void> localizingCursor() {
-		return cursor();
+	public RandomAccess<BitType> randomAccess(Interval interval) {
+		return randomAccess();
 	}
 
 	@Override
-	public long size() {
-		return codes.size();
+	public IterableInterval< Void > inside()
+	{
+		return inside;
 	}
 
-	@Override
-	public Void firstElement() {
-		return null;
-	}
+	private class InsideIterable extends AbstractWrappedInterval< Interval > implements IterableInterval< Void >
+	{
+		InsideIterable()
+		{
+			super( SparseIterableRegion.this );
+		}
 
-	@Override
-	public Object iterationOrder() {
-		return null;
-	}
+		@Override
+		public Cursor<Void> cursor() {
+			return new SparseRoiCursor();
+		}
 
-	@Override
-	public Iterator<Void> iterator() {
-		return cursor();
-	}
+		@Override
+		public Cursor<Void> localizingCursor() {
+			return cursor();
+		}
 
-	@Override
-	public RandomAccess<BitType> randomAccess() {
-		return new SparseRoiRandomAccess();
+		@Override
+		public long size() {
+			return codes.size();
+		}
+
+		@Override
+		public Void firstElement() {
+			return null;
+		}
+
+		@Override
+		public Object iterationOrder() {
+			return this;
+		}
 	}
 
 	@Override
-	public RandomAccess<BitType> randomAccess(Interval interval) {
-		return randomAccess();
+	public BitType getType()
+	{
+		return new BitType();
 	}
 
 	private class SparseRoiCursor extends AbstractCursor<Void> implements

src/main/java/sc/fiji/labkit/ui/utils/sparse/SparseRandomAccessIntType.java

@@ -78,7 +78,7 @@ public RandomAccess<IntType> randomAccess(Interval interval) {
 	}
 
 	public Cursor<IntType> sparseCursor() {
-		return new MappingCursor<>(sparsityPattern().cursor(), randomAccess());
+		return new MappingCursor<>(sparsityPattern().inside().cursor(), randomAccess());
 	}
 
 	public IterableRegion<? extends BooleanType<?>> sparsityPattern() {
@@ -124,6 +124,12 @@ private void set(MyRandomAccess position, int value) {
 		}
 	}
 
+	@Override
+	public IntType getType()
+	{
+		return new IntType();
+	}
+
 	// -- Helper classes --
 
 	private class MyRandomAccess extends Point implements RandomAccess<IntType> {

src/test/java/demo/custom_segmenter/MeanCalculator.java

@@ -45,7 +45,7 @@ class MeanCalculator {
 	public void addSample(RandomAccessibleInterval<?> image,
 		IterableRegion<BitType> region)
 	{
-		Cursor<Void> cursor = region.cursor();
+		Cursor<Void> cursor = region.inside().cursor();
 		RandomAccess<RealType<?>> randomAccess = Cast.unchecked(image.randomAccess());
 		while (cursor.hasNext()) {
 			cursor.fwd();

src/test/java/sc/fiji/labkit/ui/labeling/SparseIterableRegionTest.java

@@ -69,7 +69,7 @@ public void testSize() {
 		RandomAccess<BitType> ra = roi.randomAccess();
 		ra.setPosition(positionA);
 		ra.get().set(true);
-		assertEquals(1, roi.size());
+		assertEquals(1, roi.inside().size());
 	}
 
 	@Test
@@ -78,7 +78,7 @@ public void testCursor() {
 		RandomAccess<BitType> ra = roi.randomAccess();
 		ra.setPosition(positionA);
 		ra.get().set(true);
-		Cursor<Void> cursor = roi.cursor();
+		Cursor<Void> cursor = roi.inside().cursor();
 		assertTrue(cursor.hasNext());
 		cursor.fwd();
 		assertEquals(positionA[1], cursor.getLongPosition(1));

src/test/java/sc/fiji/labkit/ui/utils/sparse/SparseRandomAccessIntTypeTest.java

@@ -49,6 +49,6 @@ public void testNoEntryValue() {
 			noEntryValue);
 		Views.iterable(image).forEach(x -> x.setInteger(noEntryValue));
 		// test
-		assertFalse(image.sparsityPattern().cursor().hasNext());
+		assertFalse(image.sparsityPattern().inside().cursor().hasNext());
 	}
 }