Replaced potentially problematic libraries (#333)

cineast-api/src/main/java/org/vitrivr/cineast/api/util/QueryUtil.java

@@ -3,7 +3,9 @@
 import static org.vitrivr.cineast.core.util.CineastConstants.FEATURE_COLUMN_QUALIFIER;
 import static org.vitrivr.cineast.core.util.CineastConstants.GENERIC_ID_COLUMN_QUALIFIER;
 
-import gnu.trove.map.hash.TObjectDoubleHashMap;
+import com.carrotsearch.hppc.ObjectDoubleHashMap;
+import com.carrotsearch.hppc.predicates.ObjectDoublePredicate;
+import com.carrotsearch.hppc.procedures.ObjectDoubleProcedure;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -34,6 +36,7 @@
 import org.vitrivr.cineast.core.db.dao.reader.MediaSegmentReader;
 import org.vitrivr.cineast.core.db.dao.reader.TagReader;
 import org.vitrivr.cineast.core.features.SegmentTags;
+import org.vitrivr.cineast.core.features.retriever.Retriever;
 import org.vitrivr.cineast.core.temporal.TemporalScoring;
 import org.vitrivr.cineast.core.util.math.MathHelper;
 import org.vitrivr.cineast.standalone.config.Config;
@@ -171,7 +174,7 @@ public static HashMap<String, ArrayList<AbstractQueryTermContainer>> groupQueryT
   }
 
   public static List<StringDoublePair> retrieveCategory(ContinuousRetrievalLogic continuousRetrievalLogic, List<Pair<AbstractQueryTermContainer, ReadableQueryConfig>> queryContainers, String category) {
-    TObjectDoubleHashMap<String> scoreBySegmentId = new TObjectDoubleHashMap<>();
+    ObjectDoubleHashMap<String> scoreBySegmentId = new ObjectDoubleHashMap<>();
     for (Pair<AbstractQueryTermContainer, ReadableQueryConfig> pair : queryContainers) {
 
       if (pair == null) {
@@ -187,7 +190,7 @@ public static List<StringDoublePair> retrieveCategory(ContinuousRetrievalLogic c
 
     }
     final List<StringDoublePair> list = new ArrayList<>(scoreBySegmentId.size());
-    scoreBySegmentId.forEachEntry((segmentId, score) -> {
+    scoreBySegmentId.forEach((ObjectDoublePredicate<? super String>) (segmentId, score) -> {
       if (score > 0) {
         list.add(new StringDoublePair(segmentId, score));
       }
@@ -207,12 +210,12 @@ public static List<StringDoublePair> retrieveCategory(ContinuousRetrievalLogic c
 
   public static List<StringDoublePair> retrieve(ContinuousRetrievalLogic continuousRetrievalLogic, AbstractQueryTermContainer queryTermContainer, ReadableQueryConfig config, String category) {
     float weight = MathHelper.limit(queryTermContainer.getWeight(), -1f, 1f);
-    TObjectDoubleHashMap<String> scoreBySegmentId = new TObjectDoubleHashMap<>();
+    ObjectDoubleHashMap<String> scoreBySegmentId = new ObjectDoubleHashMap<>();
 
     retrieveAndWeight(continuousRetrievalLogic, category, scoreBySegmentId, queryTermContainer, config, weight);
 
     final List<StringDoublePair> list = new ArrayList<>(scoreBySegmentId.size());
-    scoreBySegmentId.forEachEntry((segmentId, score) -> {
+    scoreBySegmentId.forEach((ObjectDoublePredicate<? super String>) (segmentId, score) -> {
       if (score > 0) {
         list.add(new StringDoublePair(segmentId, score));
       }
@@ -222,7 +225,7 @@ public static List<StringDoublePair> retrieve(ContinuousRetrievalLogic continuou
     return list;
   }
 
-  private static void retrieveAndWeight(ContinuousRetrievalLogic continuousRetrievalLogic, String category, TObjectDoubleHashMap<String> scoreBySegmentId, AbstractQueryTermContainer qc, ReadableQueryConfig qconf, float weight) {
+  private static void retrieveAndWeight(ContinuousRetrievalLogic continuousRetrievalLogic, String category, ObjectDoubleHashMap<String> scoreBySegmentId, AbstractQueryTermContainer qc, ReadableQueryConfig qconf, float weight) {
     List<SegmentScoreElement> scoreResults;
     if (qc.hasId()) {
       scoreResults = continuousRetrievalLogic.retrieve(qc.getId(), category, qconf);
@@ -237,7 +240,7 @@ private static void retrieveAndWeight(ContinuousRetrievalLogic continuousRetriev
         continue;
       }
       double weightedScore = score * weight;
-      scoreBySegmentId.adjustOrPutValue(segmentId, weightedScore, weightedScore);
+      scoreBySegmentId.putOrAdd(segmentId, weightedScore, weightedScore);
     }
   }
 
@@ -275,13 +278,12 @@ public static List<Object> retrieveFeaturesForIDByCategory(String id, String cat
     final RetrievalRuntimeConfig retrievalRuntimeConfig = Config.sharedConfig().getRetriever();
     final DBSelector selector = Config.sharedConfig().getDatabase().getSelectorSupplier().get();
     List<Object> _return = new ArrayList<>();
-    retrievalRuntimeConfig.getRetrieversByCategory(category).forEachKey(retriever -> {
+    retrievalRuntimeConfig.getRetrieversByCategory(category).forEach((ObjectDoubleProcedure<? super Retriever>) (retriever, weight) -> {
       retriever.getTableNames().forEach(tableName -> {
         selector.open(tableName);
         List<Map<String, PrimitiveTypeProvider>> rows = selector.getRows(GENERIC_ID_COLUMN_QUALIFIER, new StringTypeProvider(id));
         rows.stream().map(row -> row.get(FEATURE_COLUMN_QUALIFIER).toObject()).forEach(_return::add);
       });
-      return true; // Return value false would break the foreEachKey
     });
     return _return;
   }
@@ -343,9 +345,8 @@ private static Map<String, ArrayList<HashMap<String, Object>>> getFeaturesForCat
     final RetrievalRuntimeConfig retrievalRuntimeConfig = Config.sharedConfig().getRetriever();
     Map<String, ArrayList<HashMap<String, Object>>> _return = new HashMap<>();
 
-    retrievalRuntimeConfig.getRetrieversByCategory(category).forEach(retriever -> {
+    retrievalRuntimeConfig.getRetrieversByCategory(category).forEach((ObjectDoubleProcedure<? super Retriever>) (retriever, weight) -> {
       retriever.getTableNames().forEach(tableName -> _return.put(tableName, getFeaturesFromEntity(tableName, ids)));
-      return true;
     });
 
     return _return;

cineast-core/build.gradle

@@ -90,12 +90,12 @@ dependencies {
     api group: 'com.google.code.gson', name: 'gson', version: version_gson
 
     /** Some basic stuff (collections etc). */
-    api group: "net.sf.trove4j", name: "trove4j", version: version_trove4j
     api group: "com.google.guava", name: "guava", version: version_guava
     api group: "com.googlecode.javaewah", name: "JavaEWAH", version: version_javaewah
+    api group: 'com.carrotsearch', name: 'hppc', version: vershion_hppc
 
     /** Mockito for unit testing */
-    implementation 'org.mockito:mockito-inline:4.5.1'
+    implementation 'org.mockito:mockito-inline:4.6.1'
 
     /** Tensorflow (Java). */
     if (DefaultNativePlatform.currentOperatingSystem.isMacOsX())
@@ -144,9 +144,6 @@ dependencies {
     /** OpenCV. */
     api group: 'org.openpnp', name: 'opencv', version: version_opencv
 
-    /** Evaluator of math expressions (e.g. to _evaluate_ config entries in the form of 1000/3 */
-    implementation 'com.fathzer:javaluator:3.0.3'
-
     /** Java 9+ compatibility. */
     api group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
     api group: 'javax.activation', name: 'activation', version: '1.1.1'

cineast-core/src/main/java/org/vitrivr/cineast/core/color/ColorConverter.java

@@ -1,17 +1,13 @@
 package org.vitrivr.cineast.core.color;
 
-import gnu.trove.TCollections;
-import gnu.trove.map.TIntObjectMap;
-import gnu.trove.map.hash.TIntObjectHashMap;
 
+import com.carrotsearch.hppc.IntObjectHashMap;
 
 /* for equations see http://www.easyrgb.com/ */
 public final class ColorConverter {
 
-  private static TIntObjectMap<ReadableLabContainer> rgbToLabCache = TCollections
-      .synchronizedMap(new TIntObjectHashMap<ReadableLabContainer>(100000));
-  private static TIntObjectMap<ReadableHSVContainer> rgbToHSVCache = TCollections
-      .synchronizedMap(new TIntObjectHashMap<ReadableHSVContainer>(100000));
+  private static IntObjectHashMap<ReadableLabContainer> rgbToLabCache = new IntObjectHashMap<>(100000);
+  private static IntObjectHashMap<ReadableHSVContainer> rgbToHSVCache = new IntObjectHashMap<>(100000);
 
   private ColorConverter() {
   }

cineast-core/src/main/java/org/vitrivr/cineast/core/data/FloatVectorImpl.java

@@ -1,13 +1,13 @@
 package org.vitrivr.cineast.core.data;
 
-import gnu.trove.list.array.TFloatArrayList;
+import com.carrotsearch.hppc.FloatArrayList;
 import java.util.List;
 
 public class FloatVectorImpl implements FloatVector {
 
-  private TFloatArrayList list;
+  private final FloatArrayList list;
 
-  public FloatVectorImpl(TFloatArrayList list) {
+  public FloatVectorImpl(FloatArrayList list) {
     this.list = list;
   }
 
@@ -26,7 +26,7 @@ public FloatVectorImpl(float[] array) {
   }
 
   public FloatVectorImpl() {
-    this(new TFloatArrayList());
+    this(new FloatArrayList());
   }
 
   public FloatVectorImpl(List<Double> list) {
@@ -70,7 +70,7 @@ public void add(float element) {
   }
 
   public String toFeatureString() {
-    StringBuffer buf = new StringBuffer();
+    StringBuilder buf = new StringBuilder();
     buf.append('<');
     for (int i = 0; i < this.list.size(); ++i) {
       buf.append(list.get(i));

cineast-core/src/main/java/org/vitrivr/cineast/core/data/Histogram.java

@@ -1,12 +1,12 @@
 package org.vitrivr.cineast.core.data;
 
-import gnu.trove.map.hash.TObjectIntHashMap;
+import com.carrotsearch.hppc.ObjectIntHashMap;
 import java.util.NoSuchElementException;
 
 public abstract class Histogram implements ReadableFloatVector {
 
   protected double[] bins;
-  protected TObjectIntHashMap<String> binNames = new TObjectIntHashMap<>();
+  protected ObjectIntHashMap<String> binNames = new ObjectIntHashMap<>();
 
   protected Histogram(int numberOfBins) {
     this.bins = new double[numberOfBins];
@@ -54,7 +54,7 @@ public double getDistance(Histogram hist) {
 
 
   public String toFeatureString() {
-    StringBuffer buf = new StringBuffer();
+    StringBuilder buf = new StringBuilder();
     buf.append('<');
     for (int i = 0; i < bins.length; ++i) {
       buf.append(bins[i]);

cineast-core/src/main/java/org/vitrivr/cineast/core/data/MediaType.java

@@ -1,6 +1,7 @@
 package org.vitrivr.cineast.core.data;
 
-import gnu.trove.map.hash.TIntObjectHashMap;
+
+import com.carrotsearch.hppc.IntObjectHashMap;
 import java.util.EnumSet;
 import java.util.HashMap;
 import org.apache.commons.lang3.tuple.ImmutablePair;
@@ -16,7 +17,7 @@ public enum MediaType {
   UNKNOWN(99, "u", "unknown");
 
   public static final char DELIMITER = '_';
-  private static final TIntObjectHashMap<MediaType> idToType = new TIntObjectHashMap<>();
+  private static final IntObjectHashMap<MediaType> idToType = new IntObjectHashMap<>();
   private static final HashMap<String, MediaType> prefixToType = new HashMap<>();
   private static final HashMap<String, MediaType> nameToType = new HashMap<>();
 

cineast-core/src/main/java/org/vitrivr/cineast/core/data/QueryResultCacheKey.java

@@ -1,6 +1,7 @@
 package org.vitrivr.cineast.core.data;
 
-import gnu.trove.map.hash.TObjectDoubleHashMap;
+import com.carrotsearch.hppc.ObjectDoubleHashMap;
+import java.util.Arrays;
 import java.util.Objects;
 import java.util.stream.Collectors;
 import org.vitrivr.cineast.core.config.CacheableQueryConfig;
@@ -13,18 +14,18 @@
  */
 public record QueryResultCacheKey(int queryTermContainerHash, String querySegmentId, String retrieverSpecification, CacheableQueryConfig queryConfig) {
 
-  private QueryResultCacheKey(AbstractQueryTermContainer queryTermContainer, String querySegmentId, TObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
-    this(queryTermContainer == null ? 0 : queryTermContainer.hashCode(), querySegmentId, retrievers.keySet().stream().map(retriever -> {
+  private QueryResultCacheKey(AbstractQueryTermContainer queryTermContainer, String querySegmentId, ObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
+    this(queryTermContainer == null ? 0 : queryTermContainer.hashCode(), querySegmentId, Arrays.stream(retrievers.keys().toArray(Retriever.class)).map(retriever -> {
       double weight = retrievers.get(retriever);
       return retriever.getClass().getName() + "-" + weight + "|"; //TODO disambiguate between differently configured instances of same retriever
     }).sorted().collect(Collectors.joining()), new CacheableQueryConfig(queryConfig));
   }
 
-  public QueryResultCacheKey(AbstractQueryTermContainer queryTermContainer, TObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
+  public QueryResultCacheKey(AbstractQueryTermContainer queryTermContainer, ObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
     this(queryTermContainer, null, retrievers, queryConfig);
   }
 
-  public QueryResultCacheKey(String querySegmentId, TObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
+  public QueryResultCacheKey(String querySegmentId, ObjectDoubleHashMap<Retriever> retrievers, ReadableQueryConfig queryConfig) {
     this(null, querySegmentId, retrievers, queryConfig);
   }
 

cineast-core/src/main/java/org/vitrivr/cineast/core/data/SemanticMap.java

@@ -1,6 +1,6 @@
 package org.vitrivr.cineast.core.data;
 
-import gnu.trove.map.hash.TIntObjectHashMap;
+import com.carrotsearch.hppc.IntObjectHashMap;
 import java.awt.image.BufferedImage;
 import java.util.Arrays;
 import java.util.Map;
@@ -15,7 +15,7 @@ public SemanticMap(BufferedImage image, Map<String, String> classes) {
   }
 
   private static DeepLabLabel[][] toLabels(BufferedImage image, Map<String, String> classes) {
-    TIntObjectHashMap<DeepLabLabel> intToLabelMap = new TIntObjectHashMap<>(classes.size());
+    IntObjectHashMap<DeepLabLabel> intToLabelMap = new IntObjectHashMap<>(classes.size());
     for (String className : classes.keySet()) {
 
       DeepLabLabel label;

cineast-core/src/main/java/org/vitrivr/cineast/core/data/score/ScoreElement.java

@@ -1,7 +1,8 @@
 package org.vitrivr.cineast.core.data.score;
 
+import com.carrotsearch.hppc.ObjectDoubleMap;
+import com.carrotsearch.hppc.predicates.ObjectDoublePredicate;
 import com.google.common.collect.ImmutableList;
-import gnu.trove.map.TObjectDoubleMap;
 import java.util.Comparator;
 import java.util.List;
 import java.util.stream.Stream;
@@ -27,12 +28,12 @@ static List<ScoreElement> filterMaximumScores(Stream<ScoreElement> elements) {
   }
 
   static List<SegmentScoreElement> segmentsFromSegmentsMap(
-      TObjectDoubleMap<String> scoreBySegmentId) {
+      ObjectDoubleMap<String> scoreBySegmentId) {
     return segmentsFromSegmentsDistanceMap(scoreBySegmentId, CorrespondenceFunction.identity());
   }
 
   static List<ScoreElement> scoresFromSegmentsDistanceMap(
-      TObjectDoubleMap<String> distanceBySegmentId, CorrespondenceFunction correspondence) {
+      ObjectDoubleMap<String> distanceBySegmentId, CorrespondenceFunction correspondence) {
     List<SegmentScoreElement> segments = segmentsFromSegmentsDistanceMap(distanceBySegmentId,
         correspondence);
 
@@ -41,9 +42,9 @@ static List<ScoreElement> scoresFromSegmentsDistanceMap(
   }
 
   static List<SegmentScoreElement> segmentsFromSegmentsDistanceMap(
-      TObjectDoubleMap<String> distanceBySegmentId, CorrespondenceFunction correspondence) {
+      ObjectDoubleMap<String> distanceBySegmentId, CorrespondenceFunction correspondence) {
     ImmutableList.Builder<SegmentScoreElement> builder = ImmutableList.builder();
-    distanceBySegmentId.forEachEntry((id, score) -> {
+    distanceBySegmentId.forEach((ObjectDoublePredicate<? super String>) (id, score) -> {
       builder.add(new SegmentScoreElement(id, correspondence.applyAsDouble(score)));
       return true;
     });

cineast-core/src/main/java/org/vitrivr/cineast/core/extraction/decode/m3d/STLMeshDecoder.java

@@ -1,6 +1,7 @@
 package org.vitrivr.cineast.core.extraction.decode.m3d;
 
-import gnu.trove.map.hash.TObjectIntHashMap;
+
+import com.carrotsearch.hppc.ObjectIntHashMap;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -120,7 +121,7 @@ private Mesh readAscii(InputStream is) throws IOException {
     Mesh mesh = new Mesh(100, 100);
 
     /* Prepare helper structures. */
-    TObjectIntHashMap<Vector3f> vertexBuffer = new TObjectIntHashMap<>();
+    ObjectIntHashMap<Vector3f> vertexBuffer = new ObjectIntHashMap<>();
     int index = 0;
     int[] vertexindices = new int[3];
 
@@ -212,7 +213,7 @@ private Mesh readBinary(InputStream is, int skip) throws IOException {
     Mesh mesh = new Mesh((int) triangles, (int) triangles);
 
     /* Prepare helper structures. */
-    TObjectIntHashMap<Vector3f> vertexBuffer = new TObjectIntHashMap<>();
+    ObjectIntHashMap<Vector3f> vertexBuffer = new ObjectIntHashMap<>();
     int index = 0;
     int[] vertexindices = new int[3];
 

cineast-core/src/main/java/org/vitrivr/cineast/core/features/AudioFingerprint.java

@@ -2,7 +2,8 @@
 
 import static org.vitrivr.cineast.core.util.CineastConstants.FEATURE_COLUMN_QUALIFIER;
 
-import gnu.trove.list.array.TIntArrayList;
+
+import com.carrotsearch.hppc.IntArrayList;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -48,7 +49,7 @@ public AudioFingerprint() {
 
   @Override
   public void processSegment(SegmentContainer segment) {
-    TIntArrayList filteredSpectrum = this.filterSpectrum(segment);
+    IntArrayList filteredSpectrum = this.filterSpectrum(segment);
     int vectors = filteredSpectrum.size() / FINGERPRINT;
     List<PersistentTuple> tuples = new ArrayList<>();
     for (int i = 0; i < vectors; i++) {
@@ -76,7 +77,7 @@ protected List<float[]> preprocessQuery(SegmentContainer sc, ReadableQueryConfig
     List<float[]> features = new ArrayList<>();
 
     /* Extract filtered spectrum and create query-vectors. */
-    final TIntArrayList filteredSpectrum = this.filterSpectrum(sc);
+    final IntArrayList filteredSpectrum = this.filterSpectrum(sc);
     final int shift = RANGES.length - 1;
     final int lookups = Math.max(1, Math.min(30, filteredSpectrum.size() - FINGERPRINT));
 
@@ -166,9 +167,9 @@ protected List<ReadableQueryConfig> generateQueryConfigsForFeatures(ReadableQuer
     return configs;
   }
 
-  private TIntArrayList filterSpectrum(SegmentContainer segment) {
+  private IntArrayList filterSpectrum(SegmentContainer segment) {
     /* Prepare empty list of candidates for filtered spectrum. */
-    TIntArrayList candidates = new TIntArrayList();
+    IntArrayList candidates = new IntArrayList();
 
     /* Perform STFT and extract the Spectra. If this fails, return empty list. */
     Pair<Integer, Integer> properties = FFTUtil.parametersForDuration(segment.getSamplingrate(), WINDOW_SIZE);