#4421 - Improve performance of the overlap iterator

- Fix SlidingWindow and added test

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/ner/NameSampleStream.java

@@ -23,7 +23,7 @@
 import opennlp.tools.namefind.NameSample;
 import opennlp.tools.util.ObjectStream;
 
-public class NameSampleStream
+class NameSampleStream
     implements ObjectStream<NameSample>, AutoCloseable
 {
     private List<NameSample> samples;
@@ -41,6 +41,7 @@ public NameSample read()
         if (iterator != null && iterator.hasNext()) {
             return iterator.next();
         }
+
         return null;
     }
 
@@ -56,5 +57,4 @@ public void close()
         samples = null;
         iterator = null;
     }
-
 }

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/ner/OpenNlpNerRecommender.java

@@ -161,9 +161,12 @@ public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
                 break;
             }
 
+            var firstToken = tokens.get(0);
+            var lastToken = tokens.get(tokens.size() - 1);
+
             predictionCount++;
-            predictedRangeBegin = Math.min(predictedRangeBegin, tokens.get(0).getBegin());
-            predictedRangeEnd = Math.max(predictedRangeEnd, tokens.get(tokens.size() - 1).getEnd());
+            predictedRangeBegin = Math.min(predictedRangeBegin, firstToken.getBegin());
+            predictedRangeEnd = Math.max(predictedRangeEnd, lastToken.getEnd());
 
             var tokenTexts = tokens.stream() //
                     .map(AnnotationFS::getCoveredText) //

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/ner/SlidingWindow.java

@@ -63,12 +63,12 @@ private class SlidingWindowIterator
     {
         private final Iterator<T> tokenIterator;
 
-        private List<T> nextWindow;
+        private LinkedList<T> nextWindow;
 
         public SlidingWindowIterator(Iterator<T> aTokenIterator)
         {
             tokenIterator = aTokenIterator;
-            nextWindow = makeSample(tokenIterator, new LinkedList<T>(), windowSize, windowOverlap);
+            nextWindow = makeSample(tokenIterator, new LinkedList<T>());
         }
 
         @Override
@@ -81,24 +81,29 @@ public boolean hasNext()
         public List<T> next()
         {
             var currentWindow = nextWindow;
-            nextWindow = makeSample(tokenIterator, nextWindow, windowSize, windowOverlap);
+            nextWindow = makeSample(tokenIterator, nextWindow);
             return currentWindow;
         }
 
-        private List<T> makeSample(Iterator<T> aFreshTokenIterator, List<T> aTokens, int aMaxLength,
-                int aOverlap)
+        private LinkedList<T> makeSample(Iterator<T> aFreshTokenIterator, LinkedList<T> aPrevWindow)
         {
+            var result = new LinkedList<T>();
+
             if (!aFreshTokenIterator.hasNext()) {
-                return Collections.emptyList();
+                return result;
             }
 
-            var result = new LinkedList<T>();
-
             // Add tokens overlapping with previous sample
             var size = 0;
-            if (aOverlap > 0) {
-                var overlapIterator = result.descendingIterator();
+            if (windowOverlap > 0) {
+                var overlapIterator = aPrevWindow.descendingIterator();
+
                 while (overlapIterator.hasNext()) {
+                    if (size >= windowOverlap && !result.isEmpty()) {
+                        // Overlap size reached
+                        break;
+                    }
+
                     var token = overlapIterator.next();
                     var tokenText = token.getCoveredText();
 
@@ -107,17 +112,21 @@ private List<T> makeSample(Iterator<T> aFreshTokenIterator, List<T> aTokens, int
                     }
 
                     size += tokenText.length();
-                    if (size >= aOverlap && !result.isEmpty()) {
-                        // Overlap size reached
-                        break;
-                    }
-                    result.add(0, token);
+
+                    result.add(token);
                 }
+
+                Collections.reverse(result);
             }
 
             // Add fresh tokens
             var freshTokenAdded = false;
             while (aFreshTokenIterator.hasNext()) {
+                if (size >= windowSize && freshTokenAdded) {
+                    // Maximum sample size reached
+                    break;
+                }
+
                 var token = aFreshTokenIterator.next();
                 var tokenText = token.getCoveredText();
 
@@ -126,17 +135,13 @@ private List<T> makeSample(Iterator<T> aFreshTokenIterator, List<T> aTokens, int
                 }
 
                 size += tokenText.length();
-                if (size >= aMaxLength && freshTokenAdded) {
-                    // Maximum sample size reached
-                    break;
-                }
 
                 result.add(token);
                 freshTokenAdded = true;
             }
 
             if (!freshTokenAdded) {
-                return Collections.emptyList();
+                return new LinkedList<T>();
             }
 
             return result;

inception/inception-imls-opennlp/src/test/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/ner/SlidingWindowTest.java

@@ -0,0 +1,81 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The Technische Universität Darmstadt 
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *  
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.ner;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+
+import org.apache.uima.fit.factory.JCasBuilder;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.junit.jupiter.api.Test;
+
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
+
+class SlidingWindowTest
+{
+
+    @Test
+    void test() throws Exception
+    {
+        var sentences = 10;
+        var sentenceLength = 10;
+
+        var cas = JCasFactory.createJCas();
+        var casBuilder = new JCasBuilder(cas);
+
+        var expectedTokens = new HashSet<String>();
+
+        for (int s = 0; s < sentences; s++) {
+            int sBegin = casBuilder.getPosition();
+
+            for (int t = 0; t < sentenceLength; t++) {
+                var token = String.format("%02d", s * sentenceLength + t);
+                expectedTokens.add(token);
+                casBuilder.add(token, Token.class);
+                casBuilder.add(" ");
+            }
+
+            casBuilder.add(sBegin, Sentence.class);
+            casBuilder.add(".\n");
+        }
+
+        casBuilder.close();
+
+        var sut = new SlidingWindow<>(cas.getCas(), Token.class, 20, 10);
+
+        var actualTokens = new HashSet<String>();
+        int base = 0;
+        for (var unit : sut) {
+            unit.stream().map(Token::getCoveredText).forEach(actualTokens::add);
+
+            var expected = new ArrayList<String>();
+            for (int n = 0; n < sentenceLength; n++) {
+                expected.add(String.format("%02d", base + n));
+            }
+
+            assertThat(unit.stream().map(Token::getCoveredText).toList())
+                    .containsExactlyElementsOf(expected);
+            base += sentenceLength / 2;
+        }
+
+        assertThat(actualTokens).containsExactlyInAnyOrderElementsOf(expectedTokens);
+    }
+}

inception/inception-imls-opennlp/src/test/resources/log4j2-test.xml

@@ -9,7 +9,7 @@
   <Loggers>
     <Logger name="org.deeplearning4j.optimize.listeners" level="INFO"/>
     <Logger name="de.tudarmstadt.ukp.dkpro.core.api.datasets.DatasetFactory" level="INFO"/>
-    <Logger name="de.tudarmstadt.ukp.inception.recommendation" level="TRACE"/>
+    <Logger name="de.tudarmstadt.ukp.inception.recommendation" level="INFO"/>
     <Logger name="de.tudarmstadt.ukp.inception.recommendation.api.util.OverlapIterator" level="INFO"/>
 
     <Root level="ERROR">