Merge pull request #28 from saalfeldlab/0.12.0

0.12.0

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>net.imglib2</groupId>
 	<artifactId>imglib2-label-multisets</artifactId>
-	<version>0.11.7-SNAPSHOT</version>
+	<version>0.12.0-SNAPSHOT</version>
 
 	<name>ImgLib2 Label Multisets</name>
 	<description>Implementation of label multisets as an ImgLib2 native type.</description>

src/main/java/net/imglib2/type/label/LabelMultisetEntryList.java

@@ -2,6 +2,7 @@
 
 import net.imglib2.type.label.LabelMultisetType.Entry;
 
+import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Set;
 
@@ -13,6 +14,14 @@ public LabelMultisetEntryList() {
 		super(LabelMultisetEntry.type);
 	}
 
+	@Override
+	public boolean equals(Object o) {
+		if (!(o instanceof LabelMultisetEntryList)) return false;
+		final long[] thisData = ((LongMappedAccessData) data).getData();
+		final long[] otherData = ((LongMappedAccessData) ((LabelMultisetEntryList) o).data).getData();
+		return Arrays.equals(thisData, otherData);
+	}
+
 	public LabelMultisetEntryList(final int capacity) {
 
 		super(LabelMultisetEntry.type, capacity);

src/main/java/net/imglib2/type/label/LabelMultisetType.java

@@ -72,9 +72,26 @@ private LabelMultisetType(final NativeImg<?, VolatileLabelMultisetArray> img, fi
 		this(img, access, 0);
 	}
 
+	private LabelMultisetEntry reference = null;
+
 	private LabelMultisetType(final NativeImg<?, VolatileLabelMultisetArray> img, final VolatileLabelMultisetArray access, final int idx) {
 
-		this.entries = new LabelMultisetEntryList();
+		this.entries = new LabelMultisetEntryList() {
+			@Override
+			public LabelMultisetEntry createRef() {
+				if (reference == null) {
+					return super.createRef();
+				} else return reference;
+			}
+
+			@Override
+			public void releaseRef(LabelMultisetEntry ref) {
+				if (reference != ref) {
+					super.releaseRef(ref);
+				}
+			}
+		};
+
 		this.img = img;
 		this.access = access;
 		this.i.set(idx);
@@ -100,10 +117,14 @@ public LabelMultisetEntry next() {
 					return it.next();
 				}
 
+
+
 				@Override
 				public void release() {
+					if (reference == null) {
+						it.release();
+					}
 
-					it.release();
 				}
 
 				@Override
@@ -333,38 +354,9 @@ public Set<Entry<Label>> entrySet() {
 		return entrySet;
 	}
 
-	public Set<LabelMultisetEntry> entrySetWithRef(LabelMultisetEntry ref) {
-
-		access.getValue(i.get(), entries);
-		return new AbstractSet<LabelMultisetEntry>() {
-
-			@Override
-			public Iterator<LabelMultisetEntry> iterator() {
-
-				return new Iterator<LabelMultisetEntry>() {
-
-					int idx = 0;
-
-					@Override
-					public boolean hasNext() {
-
-						return idx < size();
-					}
-
-					@Override
-					public LabelMultisetEntry next() {
-
-						return entries.get(idx++, ref);
-					}
-				};
-			}
-
-			@Override
-			public int size() {
-
-				return entries.size();
-			}
-		};
+	public Set<Entry<Label>> entrySetWithRef(LabelMultisetEntry ref) {
+		reference = ref;
+		return entrySet();
 	}
 
 	@Override

src/main/java/net/imglib2/type/label/LabelMultisetTypeDownscaler.java

@@ -77,9 +77,9 @@ public static VolatileLabelMultisetArray createDownscaledCell(
 			// populate list with all entries
 			for (int g = 0; g < numDim; ) {
 
-				randomAccess.setPosition(totalOffset);
+				final LabelMultisetType labelMultisetType = randomAccess.setPositionAndGet(totalOffset);
 
-				for (LabelMultisetEntry sourceEntry : randomAccess.get().entrySetWithRef(iteratorEntry)) {
+				for (LabelMultisetType.Entry<Label> sourceEntry : labelMultisetType.entrySetWithRef(iteratorEntry)) {
 					final long id = sourceEntry.getElement().id();
 					final int count = sourceEntry.getCount();
 					if (cellEntryMap.containsKey(id)) {

src/main/java/net/imglib2/type/label/LabelUtils.java

@@ -52,7 +52,7 @@ public static byte[] serializeLabelMultisetTypes(
 
 		final LabelMultisetEntry entryReference = new LabelMultisetEntry(0, 1);
 
-		final int entrySizeInBytes = entryReference.getSizeInBytes();
+		final int entrySizeInBytes = entryReference.getSizeInBytes(); // One Long for the element ID, and one int for the count ( 8 + 4 = 12)
 
 		final int argMaxSize = INT_SIZE; // in reality, the int value is always `0`, with size of 4 bytes
 		final int offsetListSize = INT_SIZE * numElements;
@@ -76,17 +76,16 @@ public static byte[] serializeLabelMultisetTypes(
 			if (offsetsForHash != listOffsets.getNoEntryValue()) {
 				writeInt(dataBuffer, offsetsForHash, ByteOrder.BIG_ENDIAN);
 			} else {
-				for (final LabelMultisetEntry entry : lmt.entrySetWithRef(entryReference)) {
+				for (final Entry<Label> entry : lmt.entrySetWithRef(entryReference)) {
 					/* NOTE: This is unnecessary data, but an artifact of prior serialization strategy.
 					 * It used to be that the entry we iterator from here was added to a temporary LabelMultisetEntryList
 					 * and then that list was serialized. However, the way this logic was written, the list would alawys
 					 * only contain 1 element.
 					 * We don't do this now, but unfortunately, this mean that we now how to serialize an unnecessary `1`
 					 * integer to mock the size of the list that is expected during deserialization. */
 					writeInt(entryList, 1, ByteOrder.nativeOrder()); //the old list was always only 1 element in size, stored as the first 4 bytes of a long
-					for (int i = 0; i < entrySizeInBytes; i++) {
-						entryList.write(entry.access.getByte(i));
-					}
+					writeLong(entryList, entry.getElement().id(), ByteOrder.LITTLE_ENDIAN);
+					writeInt(entryList, entry.getCount(), ByteOrder.LITTLE_ENDIAN);
 				}
 				listOffsets.put(listHash, nextListOffset);
 				writeInt(dataBuffer, nextListOffset, ByteOrder.BIG_ENDIAN);
@@ -104,6 +103,10 @@ private static void writeInt(ByteArrayOutputStream dataBuffer, int value, ByteOr
 		dataBuffer.write(ByteBuffer.allocate(4).order(byteOrder).putInt(value).array(), 0, 4);
 	}
 
+	private static void writeLong(ByteArrayOutputStream dataBuffer, long value, ByteOrder byteOrder) {
+		dataBuffer.write(ByteBuffer.allocate(8).order(byteOrder).putLong(value).array(), 0, 8);
+	}
+
 	public static LabelMultisetType getOutOfBounds() {
 
 		return getOutOfBounds(1);
@@ -143,13 +146,14 @@ public static VolatileLabelMultisetArray fromBytes(final byte[] bytes, final int
 		if (argMaxSize == 0) {
 			argMax = new long[listEntryOffsets.length];
 			final TIntLongHashMap entryOffsetToArgMax = new TIntLongHashMap(DEFAULT_CAPACITY, DEFAULT_LOAD_FACTOR, -1, -1);
+			LabelMultisetEntryList lmel = null;
 			for (int i = 0; i < listEntryOffsets.length; i++) {
 				final int listDataIdx = listEntryOffsets[i];
-				final Long cachedArgMax = entryOffsetToArgMax.get(listDataIdx);
+				final long cachedArgMax = entryOffsetToArgMax.get(listDataIdx);
 				if (cachedArgMax != entryOffsetToArgMax.getNoEntryValue()) {
 					argMax[i] = cachedArgMax;
 				} else {
-					final LabelMultisetEntryList lmel = new LabelMultisetEntryList();
+					if (lmel == null) lmel = new LabelMultisetEntryList();
 					lmel.referToDataAt(listData, listDataIdx);
 					argMax[i] = LabelUtils.getArgMax(lmel);
 					entryOffsetToArgMax.put(listDataIdx, argMax[i]);

src/main/java/net/imglib2/type/label/MappedObjectArrayList.java

@@ -17,7 +17,7 @@ public class MappedObjectArrayList<O extends MappedObject<O, T>, T extends Mappe
 
   private final O type;
 
-  private MappedAccessData<T> data;
+  protected MappedAccessData<T> data;
 
   private long baseOffset;