Merge pull request #281 from saalfeldlab/update-label-n5-dependencies

Update label multiset and N5 dependencies
saalfeldlab · Aug 5, 2019 · d5da29e · d5da29e
2 parents 7978436 + 6423817
commit d5da29e
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Showing 18 changed files with 193 additions and 187 deletions.
diff --git a/pom.xml b/pom.xml
@@ -43,11 +43,6 @@
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-common</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.janelia.saalfeldlab</groupId>
-			<artifactId>n5-label-multisets</artifactId>
-			<version>0.4.1</version>
-		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>bigdataviewer-core</artifactId>
@@ -77,6 +72,11 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-realtransform</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-label-multisets</artifactId>
+			<version>0.8.2</version>
+		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>bigdataviewer-vistools</artifactId>
@@ -94,17 +94,17 @@
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5</artifactId>
-			<version>2.0.2</version>
+			<version>2.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-hdf5</artifactId>
-			<version>1.0.3</version>
+			<version>1.0.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-imglib2</artifactId>
-			<version>3.0.0</version>
+			<version>3.4.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/PainteraShowContainer.java b/src/main/java/org/janelia/saalfeldlab/paintera/PainteraShowContainer.java
@@ -31,6 +31,7 @@
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
+import org.janelia.saalfeldlab.n5.imglib2.N5LabelMultisets;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.paintera.composition.ARGBCompositeAlphaAdd;
 import org.janelia.saalfeldlab.paintera.composition.ARGBCompositeAlphaYCbCr;
@@ -98,7 +99,6 @@
 import net.imglib2.converter.ARGBCompositeColorConverter;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.type.NativeType;
-import net.imglib2.type.label.LabelUtils;
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.volatiles.AbstractVolatileRealType;
@@ -739,7 +739,7 @@ private static <I extends IntegerType<I> & NativeType<I>> void findMaxId(
 					? N5Helpers.getFinestLevelJoinWithGroup(reader, group)
 					: group;
 		final boolean isLabelMultiset = N5Helpers.getBooleanAttribute(reader, dataset, N5Helpers.IS_LABEL_MULTISET_KEY, false);
-		final CachedCellImg<I, ?> img = isLabelMultiset ? (CachedCellImg<I, ?>) (CachedCellImg) LabelUtils.openVolatile(reader, dataset) : (CachedCellImg<I, ?>) N5Utils.open(reader, dataset);
+		final CachedCellImg<I, ?> img = isLabelMultiset ? (CachedCellImg<I, ?>) (CachedCellImg) N5LabelMultisets.openLabelMultiset(reader, dataset) : N5Utils.open(reader, dataset);
 		final int[] blockSize = new  int[img.numDimensions()];
 		img.getCellGrid().cellDimensions(blockSize);
 		final List<Interval> blocks = Grids.collectAllContainedIntervals(img.getCellGrid().getImgDimensions(), blockSize);

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationMode.java b/src/main/java/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationMode.java
@@ -158,7 +158,7 @@ private static final class SectionInfo
 
 	private static final Color MASK_COLOR = Color.web("00CCFF");
 
-	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.regular(t.get()) && t.get() != Label.BACKGROUND;
+	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.isForeground(t.get());
 
 	private final MaskedSource<D, ?> source;
 	private final LabelSourceState<D, ?> sourceState;

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/control/paint/PaintActions2D.java b/src/main/java/org/janelia/saalfeldlab/paintera/control/paint/PaintActions2D.java
@@ -164,7 +164,7 @@ public void applyMask()
 
 	}
 
-	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.regular(t.get()) && t.get() != Label.BACKGROUND;
+	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.isForeground(t.get());
 
 	private final ViewerPanelFX viewer;
 

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/control/paint/PaintClickOrDrag.java b/src/main/java/org/janelia/saalfeldlab/paintera/control/paint/PaintClickOrDrag.java
@@ -72,7 +72,7 @@ public String toString()
 		}
 	}
 
-	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.regular(t.get()) && t.get() != Label.BACKGROUND;
+	private static final Predicate<UnsignedLongType> FOREGROUND_CHECK = t -> Label.isForeground(t.get());
 
 	private final SourceInfo sourceInfo;
 

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/Masks.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/Masks.java
@@ -4,10 +4,13 @@
 import java.nio.file.Paths;
 import java.util.Optional;
 import java.util.concurrent.ExecutorService;
-import java.util.function.BiConsumer;
 import java.util.function.Supplier;
 
-import net.imglib2.cache.img.CachedCellImg;
+import org.janelia.saalfeldlab.paintera.data.DataSource;
+import org.janelia.saalfeldlab.paintera.data.mask.persist.PersistCanvas;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import net.imglib2.img.cell.AbstractCellImg;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.label.FromIntegerTypeConverter;
@@ -19,10 +22,6 @@
 import net.imglib2.type.numeric.integer.UnsignedLongType;
 import net.imglib2.type.volatiles.AbstractVolatileRealType;
 import net.imglib2.type.volatiles.VolatileUnsignedLongType;
-import org.janelia.saalfeldlab.paintera.data.DataSource;
-import org.janelia.saalfeldlab.paintera.data.mask.persist.PersistCanvas;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 public class Masks
 {
@@ -204,12 +203,12 @@ public static MaskedSource<LabelMultisetType, VolatileLabelMultisetType> fromLab
 			}
 		}
 
-		final LabelMultisetType defaultValue = FromIntegerTypeConverter.geAppropriateType();
+		final LabelMultisetType defaultValue = FromIntegerTypeConverter.getAppropriateType();
 		new FromIntegerTypeConverter<UnsignedLongType>().convert(new UnsignedLongType(Label.INVALID), defaultValue);
 
-		final LabelMultisetType type = FromIntegerTypeConverter.geAppropriateType();
+		final LabelMultisetType type = FromIntegerTypeConverter.getAppropriateType();
 		new FromIntegerTypeConverter<UnsignedLongType>().convert(new UnsignedLongType(Label.OUTSIDE), defaultValue);
-		final VolatileLabelMultisetType vtype = FromIntegerTypeConverter.geAppropriateVolatileType();
+		final VolatileLabelMultisetType vtype = FromIntegerTypeConverter.getAppropriateVolatileType();
 		new FromIntegerTypeConverter<UnsignedLongType>().convert(new UnsignedLongType(Label.OUTSIDE), defaultValue);
 		vtype.setValid(true);
 

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/PickOneLabelMultisetType.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/PickOneLabelMultisetType.java
@@ -3,12 +3,13 @@
 import java.util.function.BiPredicate;
 import java.util.function.Predicate;
 
+import org.janelia.saalfeldlab.paintera.data.mask.PickOne.PickAndConvert;
+
 import net.imglib2.converter.Converter;
 import net.imglib2.type.label.FromIntegerTypeConverter;
 import net.imglib2.type.label.LabelMultisetType;
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.util.Triple;
-import org.janelia.saalfeldlab.paintera.data.mask.PickOne.PickAndConvert;
 
 public class PickOneLabelMultisetType<M extends IntegerType<M>>
 		implements PickOne.PickAndConvert<LabelMultisetType, M, M, LabelMultisetType>
@@ -27,7 +28,7 @@ public PickOneLabelMultisetType(final Predicate<M> pickThird, final BiPredicate<
 		super();
 		this.pickThird = pickThird;
 		this.pickSecond = pickSecond;
-		this.scalarValue = FromIntegerTypeConverter.geAppropriateType();
+		this.scalarValue = FromIntegerTypeConverter.getAppropriateType();
 		this.converter = new FromIntegerTypeConverter<>();
 	}
 

diff --git a/...ain/java/org/janelia/saalfeldlab/paintera/data/mask/PickOneVolatileLabelMultisetType.java b/...ain/java/org/janelia/saalfeldlab/paintera/data/mask/PickOneVolatileLabelMultisetType.java
@@ -3,14 +3,15 @@
 import java.util.function.BiPredicate;
 import java.util.function.Predicate;
 
+import org.janelia.saalfeldlab.paintera.data.mask.PickOne.PickAndConvert;
+
 import net.imglib2.Volatile;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.label.FromIntegerTypeConverter;
 import net.imglib2.type.label.LabelMultisetType;
 import net.imglib2.type.label.VolatileLabelMultisetType;
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.util.Triple;
-import org.janelia.saalfeldlab.paintera.data.mask.PickOne.PickAndConvert;
 
 public class PickOneVolatileLabelMultisetType<M extends IntegerType<M>, VM extends Volatile<M>>
 		implements PickOne.PickAndConvert<VolatileLabelMultisetType, VM, VM, VolatileLabelMultisetType>
@@ -29,7 +30,7 @@ public PickOneVolatileLabelMultisetType(final Predicate<M> pickThird, final BiPr
 		super();
 		this.pickThird = pickThird;
 		this.pickSecond = pickSecond;
-		this.scalarValue = FromIntegerTypeConverter.geAppropriateVolatileType();
+		this.scalarValue = FromIntegerTypeConverter.getAppropriateVolatileType();
 		this.converter = new FromIntegerTypeConverter<>();
 	}
 

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/n5/BackgroundCanvasIterable.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/n5/BackgroundCanvasIterable.java
@@ -1,14 +1,14 @@
 package org.janelia.saalfeldlab.paintera.data.n5;
 
+import java.util.Iterator;
+
 import net.imglib2.converter.Converter;
 import net.imglib2.type.label.FromIntegerTypeConverter;
 import net.imglib2.type.label.Label;
 import net.imglib2.type.label.LabelMultisetType;
 import net.imglib2.type.numeric.integer.UnsignedLongType;
 import net.imglib2.util.Pair;
 
-import java.util.Iterator;
-
 /**
  * @author Philipp Hanslovsky
  *
@@ -26,7 +26,7 @@ public class BackgroundCanvasIterable implements Iterable<LabelMultisetType> {
 	 * @param backgroundAndCanvas {@link Iterable} over pairs of background ({@link LabelMultisetType})
 	 *                                               and canvas ({@link UnsignedLongType}).
 	 */
-	public BackgroundCanvasIterable(Iterable<? extends Pair<LabelMultisetType, UnsignedLongType>> backgroundAndCanvas) {
+	public BackgroundCanvasIterable(final Iterable<? extends Pair<LabelMultisetType, UnsignedLongType>> backgroundAndCanvas) {
 		this.backgroundAndCanvas = backgroundAndCanvas;
 	}
 
@@ -38,7 +38,7 @@ public Iterator<LabelMultisetType> iterator() {
 
 			final Converter<UnsignedLongType, LabelMultisetType> conv = new FromIntegerTypeConverter<>();
 
-			final LabelMultisetType type = FromIntegerTypeConverter.geAppropriateType();
+			final LabelMultisetType type = FromIntegerTypeConverter.getAppropriateType();
 
 			@Override
 			public boolean hasNext() {