Imglib roi io support

pom.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="https://maven.apache.org/POM/4.0.0" xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -15,6 +15,8 @@
 
 		<!-- NB: Deploy releases to the ImageJ Maven repository. -->
 		<releaseProfiles>deploy-to-scijava</releaseProfiles>
+		<imglib2-roi.version>0.11.0</imglib2-roi.version>
+		<imglib2-roi-io.version>0.2.0-SNAPSHOT</imglib2-roi-io.version>
 	</properties>
 
 	<groupId>com.indago</groupId>
@@ -50,6 +52,15 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-ij</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-roi</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-roi-io</artifactId>
+			<version>${imglib2-roi-io.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>nz.ac.waikato.cms.weka</groupId>
 			<artifactId>weka-dev</artifactId>
@@ -141,11 +152,11 @@
 	<repositories>
 		<repository>
 			<id>imagej.public</id>
-			<url>http://maven.scijava.org/content/groups/public</url>
+			<url>https://maven.scijava.org/content/groups/public</url>
 		</repository>
 		<repository>
 			<id>erichseifert.de</id>
-			<url>http://mvn.erichseifert.de/maven2</url>
+			<url>https://mvn.erichseifert.de/maven2</url>
 		</repository>
 	</repositories>
 </project>

src/main/java/com/indago/data/segmentation/LabelData.java

@@ -1,5 +1,7 @@
 package com.indago.data.segmentation;
 
+import gnu.trove.list.TIntList;
+import gnu.trove.list.array.TIntArrayList;
 import java.util.ArrayList;
 
 /**
@@ -22,7 +24,9 @@ public class LabelData {
 
 	private LabelingTreeNode labelingTreeNode;
 
-	private final ArrayList< Integer > fragmentIndices;
+	private final TIntList fragmentIndices;
+
+	private String segmentSource;
 
 	LabelData() {
 		this( createId() );
@@ -33,7 +37,8 @@ public class LabelData {
 		useId( id );
 		segment = null;
 		labelingTreeNode = null;
-		fragmentIndices = new ArrayList<>();
+		fragmentIndices = new TIntArrayList();
+		segmentSource = null;
 	}
 
 	void setSegment( final LabelingSegment segment ) {
@@ -52,7 +57,7 @@ public LabelingTreeNode getLabelingTreeNode() {
 		return labelingTreeNode;
 	}
 
-	public ArrayList< Integer > getFragmentIndices() {
+	public TIntList getFragmentIndices() {
 		return fragmentIndices;
 	}
 
@@ -70,4 +75,14 @@ private static synchronized void useId( final int id ) {
 		if ( nextId < id + 1 )
 			nextId = id + 1;
 	}
+
+	public void setSegmentSource( String source ) {
+		this.segmentSource = source;
+
+	}
+
+	public String getSegmentSource() {
+		return segmentSource;
+	}
+
 }

src/main/java/com/indago/data/segmentation/LabelingBuilder.java

@@ -30,7 +30,22 @@ public LabelingBuilder( final LabelingPlus labelingPlus ) {
 		super( labelingPlus );
 	}
 
-	public synchronized < T extends TreeNode< T > & Iterable< ? extends Localizable > > LabelingForest buildLabelingForest( final Forest< T > forest ) {
+	public synchronized < T extends TreeNode< T > & Iterable< ? extends Localizable > > LabelingForest buildLabelingForest(
+			final Forest< T > forest ) {
+		String segmentationSource = "";
+		return buildingLabelingForestWithSegmentationSource( forest, segmentationSource );
+	}
+
+	private < T extends TreeNode< T > & Iterable< ? extends Localizable > > LabelingForest buildingLabelingForestWithSegmentationSource(
+			final Forest< T > forest,
+			String segmentationSource ) {
+
+		return buildingLabelingForestWithSegmentationSource( forest, segmentationSource );
+	}
+
+	public synchronized < T extends TreeNode< T > & Iterable< ? extends Localizable > > LabelingForest buildLabelingForest(
+			final Forest< T > forest,
+			String segmentationSource ) {
 		// invalidate fragments and segments because we will add new labels
 		fragments = null;
 		segments = null;
@@ -61,7 +76,7 @@ public LabelingBuilder( final LabelingPlus labelingPlus ) {
 		// build a LabelingForest using the structure of the original forest
 		final HashSet< LabelingTreeNode > roots = new HashSet<>();
 		for ( final T node : forest.roots() )
-			roots.add( buildLabelingTreeNodeFor( node, nodeToLabel ) );
+			roots.add( buildLabelingTreeNodeFor( node, nodeToLabel, segmentationSource ) );
 
 		// add new forest to list of forests ever added
 		final LabelingForest labelingForest = new LabelingForest( roots );
@@ -70,12 +85,15 @@ public LabelingBuilder( final LabelingPlus labelingPlus ) {
 		return labelingForest;
 	}
 
-	private < T extends TreeNode< T > > LabelingTreeNode buildLabelingTreeNodeFor( final T node, final HashMap< T, LabelData > nodeToLabel ) {
+	private < T extends TreeNode< T > > LabelingTreeNode buildLabelingTreeNodeFor(
+			final T node,
+			final HashMap< T, LabelData > nodeToLabel,
+			final String segmentationSource ) {
 		final LabelData label = nodeToLabel.get( node );
-		createSegmentAndTreeNode( label );
+		createSegmentAndTreeNode( label, segmentationSource );
 		final LabelingTreeNode ltn = label.getLabelingTreeNode();
 		for ( final T c : node.getChildren() )
-			ltn.addChild( buildLabelingTreeNodeFor( c, nodeToLabel ) );
+			ltn.addChild( buildLabelingTreeNodeFor( c, nodeToLabel, segmentationSource ) );
 		return ltn;
 	}
 }

src/main/java/com/indago/data/segmentation/LabelingPlus.java

@@ -1,14 +1,18 @@
 package com.indago.data.segmentation;
 
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 
+import java.util.Set;
+import net.imglib2.Cursor;
 import net.imglib2.Dimensions;
 import net.imglib2.img.Img;
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.roi.labeling.LabelRegion;
 import net.imglib2.roi.labeling.LabelRegions;
 import net.imglib2.roi.labeling.LabelingMapping;
+import net.imglib2.roi.labeling.LabelingType;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.util.Util;
 
@@ -34,13 +38,20 @@ public class LabelingPlus
 	public LabelingPlus( final Dimensions dimensions ) {
 		indexImg = Util.getArrayOrCellImgFactory( dimensions, intType ).create( dimensions, intType );
 		labeling = new ImgLabeling<>( indexImg );
-		labelRegions = new LabelRegions< LabelData >( labeling );
-		labelingForests = new ArrayList< LabelingForest >();
+		labelRegions = new LabelRegions<>( labeling );
+		labelingForests = new ArrayList<>();
 	}
 
 	public LabelingPlus( final Img< IntType > indexImg ) {
 		this.indexImg = indexImg;
 		labeling = new ImgLabeling<>( indexImg );
+		labelRegions = new LabelRegions<>( labeling );
+		labelingForests = new ArrayList<>();
+	}
+
+	public LabelingPlus( final Img< IntType > indexImg, final ImgLabeling labeling ) {
+		this.indexImg = indexImg;
+		this.labeling = labeling;
 		labelRegions = new LabelRegions< LabelData >( labeling );
 		labelingForests = new ArrayList< LabelingForest >();
 	}
@@ -69,7 +80,8 @@ public synchronized ArrayList< LabelingFragment > getFragments() {
 		if ( fragments == null ) {
 			fragments = new ArrayList<>();
 			final LabelingMapping< LabelData > mapping = labeling.getMapping();
-			for ( final LabelData label : mapping.getLabels() )
+			final Set< LabelData > labels = mapping.getLabels();
+			for ( final LabelData label : labels )
 				label.getFragmentIndices().clear();
 			final int numLabelSets = mapping.numSets();
 			final boolean[] flags = new boolean[ numLabelSets ];
@@ -99,12 +111,58 @@ public synchronized ArrayList< LabelingSegment > getSegments() {
 		return segments;
 	}
 
-	void createSegmentAndTreeNode( final LabelData label )
+	void createSegmentAndTreeNode( final LabelData label, final String source )
 	{
-		final LabelRegion< LabelData > labelRegion = labelRegions.getLabelRegion( label );
-		final LabelingSegment segment = new LabelingSegment( labelRegion );
+		final LabelingSegment segment = new LabelingSegment( () -> labelRegions.getLabelRegion( label ) );
 		label.setSegment( segment );
+		label.setSegmentSource( source );
 		final LabelingTreeNode ltn = new LabelingTreeNode( segment, label );
 		label.setLabelingTreeNode( ltn );
 	}
+
+	/**
+	 * "Compress" labeling by removing (from mapping and index image) label sets that don't occur in the index image.
+	 * <p>
+	 * TODO:
+	 *  - move to imglib2-roi ImgLabeling
+	 *  - parallelize indexImg remapping using Parallelization/LoopBuilder
+	 *  - increment modcount
+	 */
+	public synchronized void pack()
+	{
+		final LabelingMapping< LabelData > mapping = labeling.getMapping();
+
+		// indexMap[ oldIndex ] == newIndex
+		final int[] indexMap = new int[ mapping.numSets() ];
+		final int[] inverseIndexMap = new int[ mapping.numSets() ];
+
+		int nextIndex = 1;
+		final Cursor< IntType > c = indexImg.cursor();
+		while ( c.hasNext() )
+		{
+			final IntType type = c.next();
+			final int oldIndex = type.get();
+			if ( oldIndex != 0 )
+			{
+				int newIndex = indexMap[ oldIndex ];
+				if ( newIndex == 0 )
+				{
+					newIndex = nextIndex++;
+					indexMap[ oldIndex ] = newIndex;
+					inverseIndexMap[ newIndex ] = oldIndex;
+				}
+				type.set( newIndex );
+			}
+		}
+		final int numLabelSets = nextIndex;
+
+		final List< Set< LabelData > > labelSets = new ArrayList<>( numLabelSets );
+		labelSets.add( new HashSet<>() );
+		for ( int i = 1; i < numLabelSets; i++ )
+			labelSets.add( new HashSet<>( mapping.labelsAtIndex( inverseIndexMap[ i ] ) ) );
+		mapping.setLabelSets( labelSets );
+
+		LabelingType< LabelData > t = labeling.firstElement();
+		t.set( t );
+	}
 }

src/main/java/com/indago/data/segmentation/LabelingSegment.java

@@ -1,5 +1,6 @@
 package com.indago.data.segmentation;
 
+import java.util.function.Supplier;
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccess;
 import net.imglib2.RealLocalizable;
@@ -16,10 +17,12 @@
  */
 public class LabelingSegment implements Segment {
 
-	private final LabelRegion< LabelData > region;
+	private final Supplier< LabelRegion< LabelData > > regionSupplier;
 
-	protected LabelingSegment( final LabelRegion< LabelData > region ) {
-		this.region = region;
+	private LabelRegion< LabelData > region = null;
+
+	protected LabelingSegment( final Supplier< LabelRegion< LabelData > > region ) {
+		this.regionSupplier = region;
 	}
 
 	/**
@@ -30,23 +33,23 @@ protected LabelingSegment( final LabelRegion< LabelData > region ) {
 	 * @return unique serialization id of the backing {@code LabelRegion}.
 	 */
 	public int getId() {
-		return region.getLabel().getId();
+		return region().getLabel().getId();
 	}
 
 	@Override
 	public long getArea() {
-		return region.size();
+		return region().size();
 	}
 
 	@Override
 	public RealLocalizable getCenterOfMass() {
-		return region.getCenterOfMass();
+		return region().getCenterOfMass();
 	}
 
 	@Override
 	public IterableRegion< ? > getRegion()
 	{
-		return region;
+		return region();
 	}
 
 	/**
@@ -57,10 +60,10 @@ public RealLocalizable getCenterOfMass() {
 	public boolean conflictsWith( final Segment segment ) {
 		final IterableRegion< ? > segmentRegion = segment.getRegion();
 		if ( segment instanceof LabelingSegment )
-			if ( Intervals.isEmpty( Intervals.intersect( this.region, segmentRegion ) ) )
+			if ( Intervals.isEmpty( Intervals.intersect( this.region(), segmentRegion ) ) )
 				return false;
 
-		final RandomAccess< BoolType > raMask = region.randomAccess();
+		final RandomAccess< BoolType > raMask = region().randomAccess();
 		final Cursor< ? > cSegment = segmentRegion.cursor();
 		while ( cSegment.hasNext() ) {
 			cSegment.fwd();
@@ -84,4 +87,21 @@ public String toString() {
 		}
 		return ret;
 	}
+
+	public String getSegmentationSource() {
+		return region.getLabel().getSegmentSource();
+	}
+
+	private LabelRegion< LabelData > region()
+	{
+		if ( region == null )
+		{
+			synchronized ( this )
+			{
+				if ( region == null )
+					region = regionSupplier.get();
+			}
+		}
+		return region;
+	}
 }

src/main/java/com/indago/data/segmentation/MinimalOverlapConflictGraph.java

@@ -1,5 +1,6 @@
 package com.indago.data.segmentation;
 
+import gnu.trove.list.TIntList;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -68,8 +69,8 @@ public static ArrayList< ArrayList< LabelingSegment > > getConflictGraphCliques(
 					Arrays.fill( heads, 1, numLists, 0 );
 				heads[ 0 ] = -1;
 				int currListIndex, firstListElem, currListElem;
-				ArrayList< Integer > currList;
-				final ArrayList< Integer > firstList = intersect.get( 0 ).getFragmentIndices();
+				TIntList currList;
+				final TIntList firstList = intersect.get( 0 ).getFragmentIndices();
 				A2: while ( true ) {
 					if ( ++heads[ 0 ] >= firstList.size() ) {
 						// done. we found all elements of the intersection.

src/main/java/com/indago/data/segmentation/PairwiseConflictGraph.java

@@ -1,5 +1,6 @@
 package com.indago.data.segmentation;
 
+import gnu.trove.list.TIntList;
 import java.util.ArrayList;
 import java.util.Collection;
 
@@ -36,7 +37,10 @@ public static ArrayList< ArrayList< LabelingSegment > > getConflictGraphCliques(
 			final LabelData sli = segmentLabels.get( i );
 			for ( int j = i + 1; j < numSegments; ++j ) {
 				final LabelData slj = segmentLabels.get( j );
-				for ( final Integer fj : slj.getFragmentIndices() ) {
+				final TIntList fragmentIndices = slj.getFragmentIndices();
+				for ( int k = 0; k < fragmentIndices.size(); k++ )
+				{
+					int fj = fragmentIndices.get( k );
 					if ( sli.getFragmentIndices().contains( fj ) ) {
 						final ArrayList< LabelingSegment > clique = new ArrayList<>();
 						clique.add( sli.getSegment() );