Merge pull request #35 from saalfeldlab/fix/serializationHashCollision

Fix/serialization hash collision

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

@@ -0,0 +1,58 @@
+package net.imglib2.type.label;
+
+class ComparableLabelMultisetEntryList extends LabelMultisetEntryList implements Comparable<LabelMultisetEntryList> {
+
+	private final LabelMultisetEntry ref;
+
+	ComparableLabelMultisetEntryList() {
+		this(new LabelMultisetEntry());
+	}
+
+	ComparableLabelMultisetEntryList(final LabelMultisetEntry ref) {
+
+		this.ref = ref;
+	}
+
+	ComparableLabelMultisetEntryList(final LabelMultisetEntryList list) {
+		this(list, new LabelMultisetEntry());
+
+	}
+	ComparableLabelMultisetEntryList(final LabelMultisetEntryList list, final LabelMultisetEntry ref) {
+
+		this.ref = ref;
+		referToDataAt(list.data, list.getBaseOffset());
+	}
+
+	@Override public LabelMultisetEntry createRef() {
+
+		return ref;
+	}
+
+	@Override public int compareTo(LabelMultisetEntryList o) {
+
+		final int size = size();
+
+		/* if different sizes or empty, return result of compare size*/
+		final int sizeCompare = Integer.compare(size, o.size());
+		if (sizeCompare != 0 || size == 0)
+			return sizeCompare;
+
+		final RefIterator<LabelMultisetEntry> thisIter = iterator();
+		final RefIterator<LabelMultisetEntry> otherIter = o.iterator();
+
+		for (int i = 0; i < size; i++) {
+			final LabelMultisetEntry thisNext = thisIter.next();
+			final LabelMultisetEntry otherNext = otherIter.next();
+
+			final int idCompare = Long.compare(thisNext.getId(), otherNext.getId());
+			if (idCompare != 0)
+				return idCompare;
+
+			final int countCompare = Integer.compare(thisNext.getCount(), otherNext.getCount());
+			if (countCompare != 0)
+				return countCompare;
+		}
+
+		return 0;
+	}
+}

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

@@ -3,7 +3,6 @@
 import net.imglib2.type.label.LabelMultisetType.Entry;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Iterator;
 import java.util.Set;
@@ -43,9 +42,9 @@ public boolean equals(Object o) {
 		if (!(o instanceof LabelMultisetEntryList)) return false;
 		final LabelMultisetEntryList other = (LabelMultisetEntryList)o;
 		if (other.size() != size()) return false;
-		final long[] thisData = ((LongMappedAccessData) data).getData();
-		final long[] otherData = ((LongMappedAccessData) other.data).getData();
-		return Arrays.equals(thisData, otherData);
+		final ComparableLabelMultisetEntryList thisComparable = new ComparableLabelMultisetEntryList(this);
+		final ComparableLabelMultisetEntryList otherComparable = new ComparableLabelMultisetEntryList(other);
+		return thisComparable.compareTo(otherComparable) == 0;
 	}
 
 	public LabelMultisetEntryList(final int capacity) {

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

@@ -287,8 +287,7 @@ public LabelMultisetType copy() {
 					access.isValid(),
 					access.argMaxCopy());
 			/* get a new type instance */
-			final LabelMultisetType that = new LabelMultisetType(null, accessCopy);
-			return that;
+			return new LabelMultisetType(null, accessCopy);
 		}
 	}
 
@@ -702,10 +701,16 @@ public int compareTo(final LabelMultisetType arg0) {
 
 		final long ours = argMax();
 		final long theirs = arg0.argMax();
-		final int initialComparison = Long.compare(ours, theirs);
 
-		if (initialComparison != 0) return initialComparison;
-		else return Long.compare(count(ours), count(theirs));
+		final int argMaxCompare = Long.compare(ours, theirs);
+		if (argMaxCompare != 0) return argMaxCompare;
+
+		final int countCompare = Long.compare(count(ours), count(theirs));
+		if (countCompare != 0) return countCompare;
+
+		final ComparableLabelMultisetEntryList thisComparable = new ComparableLabelMultisetEntryList(labelMultisetEntries());
+		final ComparableLabelMultisetEntryList otherComparable = new ComparableLabelMultisetEntryList(arg0.labelMultisetEntries());
+		return thisComparable.compareTo(otherComparable);
 	}
 
 	@Override

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

@@ -1,7 +1,5 @@
 package net.imglib2.type.label;
 
-import gnu.trove.impl.Constants;
-import gnu.trove.map.hash.TIntIntHashMap;
 import gnu.trove.map.hash.TIntLongHashMap;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.Converters;
@@ -15,12 +13,13 @@
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.util.Collection;
+import java.util.Set;
+import java.util.TreeMap;
 
 import static gnu.trove.impl.Constants.DEFAULT_CAPACITY;
 import static gnu.trove.impl.Constants.DEFAULT_LOAD_FACTOR;
 import static net.imglib2.type.label.AbstractLabelMultisetLoader.argMaxListSizeInBytes;
 import static net.imglib2.type.label.AbstractLabelMultisetLoader.listOffsetsSizeInBytes;
-import static net.imglib2.type.label.ByteUtils.INT_SIZE;
 
 public class LabelUtils {
 
@@ -52,40 +51,47 @@ public static byte[] serializeLabelMultisetTypes(
 
 		final LabelMultisetEntry entryReference = new LabelMultisetEntry(0, 1);
 
-		final int argMaxSize = INT_SIZE; // in reality, the int value is always `0`, with size of 4 bytes
-		final int offsetListSize = INT_SIZE * numElements;
 		final ByteArrayOutputStream dataBuffer = new ByteArrayOutputStream();
 		/* No longer serialized out ArgMax; we do this by specifying the ArgMax size as 0;
 		 * It's now calculated during deserializtaion instead.*/
 		writeInt(dataBuffer, 0, ByteOrder.BIG_ENDIAN);
 
-		final TIntIntHashMap listOffsets = new TIntIntHashMap(DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, -1);
+		final TreeMap<ComparableLabelMultisetEntryList, Integer> listOffsets = new TreeMap<>();
 
 		int nextListOffset = 0;
 
-		int nonEmptyListCount = 0;
+		boolean allListsEmpty = true;
 
 		final ByteArrayOutputStream entryList = new ByteArrayOutputStream();
+		ComparableLabelMultisetEntryList listRef = new ComparableLabelMultisetEntryList();
 		for (final LabelMultisetType lmt : lmts) {
-			if (!(lmt.isEmpty() || (lmt.size() == 0) ))
-				nonEmptyListCount++;
-			final int listHash = lmt.listHashCode();
-			int listOffset = listOffsets.get(listHash);
-			if (listOffset != listOffsets.getNoEntryValue()) {
+
+			lmt.getAccess().getValue(lmt.index().get(), listRef);
+			final Integer listOffset = listOffsets.putIfAbsent(listRef, nextListOffset);
+			if (listOffset != null) {
 				writeInt(dataBuffer, listOffset, ByteOrder.BIG_ENDIAN);
 			} else {
-				writeInt(entryList, lmt.entrySet().size(), ByteOrder.LITTLE_ENDIAN);
-				for (final Entry<Label> entry : lmt.entrySetWithRef(entryReference)) {
+				/* deep copy the list (in-place) ONLY if we are a new list just added to the treeView */
+				final ComparableLabelMultisetEntryList swap = new ComparableLabelMultisetEntryList();
+				swap.addAll(listRef);
+				listRef.referToDataAt(swap.data, swap.getBaseOffset());
+				listRef = swap;
+
+				final Set<Entry<Label>> entries = lmt.entrySetWithRef(entryReference);
+				writeInt(entryList, entries.size(), ByteOrder.LITTLE_ENDIAN);
+				for (final Entry<Label> entry : entries) {
 					writeLong(entryList, entry.getElement().id(), ByteOrder.LITTLE_ENDIAN);
-					writeInt(entryList, entry.getCount(), ByteOrder.LITTLE_ENDIAN);
+					final int count = entry.getCount();
+					writeInt(entryList, count, ByteOrder.LITTLE_ENDIAN);
+
+					allListsEmpty = allListsEmpty && count == 0;
 				}
-				listOffsets.put(listHash, nextListOffset);
 				writeInt(dataBuffer, nextListOffset, ByteOrder.BIG_ENDIAN);
 				nextListOffset = entryList.size(); //Another quirk to maintain size compatibility, see list NOTE above.
 			}
 		}
 
-		if (nonEmptyListCount == 0)
+		if (allListsEmpty)
 			return null;
 
 		final byte[] entryListBytes = entryList.toByteArray();

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

@@ -112,6 +112,8 @@ public int getArrayLength() {
 
   public long argMax(final int offset) {
 
+  	if (data.length == 0)
+	  return Label.INVALID;
 	return this.argMax[offset];
   }