Slight code quality improvements.

elki-project · Feb 17, 2024 · 262b4ef · 262b4ef
1 parent 2c11055
commit 262b4ef
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Showing 9 changed files with 47 additions and 72 deletions.
diff --git a/.github/codeql-config.yml b/.github/codeql-config.yml
@@ -20,3 +20,5 @@ query-filters:
     id: java/class-name-matches-super-class # Par, Instance, Factory...
 - exclude:
     id: java/comparison-of-identical-expressions # NaN checks
+- exclude:
+    id: java/uncontrolled-arithmetic # many false reports
diff --git a/elki-core-data/src/main/java/elki/data/type/MultivariateSeriesTypeInformation.java b/elki-core-data/src/main/java/elki/data/type/MultivariateSeriesTypeInformation.java
@@ -51,7 +51,6 @@ public static <V extends FeatureVector<?>> MultivariateSeriesTypeInformation<V>
   /**
    * Constructor for an actual type.
    *
-   * @param <V> vector type
    * @param cls base class
    * @param mindim Minimum dimensionality
    * @param maxdim Maximum dimensionality

diff --git a/elki-gui-minigui/src/main/java/elki/gui/util/ClassTree.java b/elki-gui-minigui/src/main/java/elki/gui/util/ClassTree.java
@@ -180,6 +180,11 @@ public PackageNode(String display, String pkgname) {
     public String getPackageName() {
       return pkgname;
     }
+
+    @Override
+    public Object clone() {
+      return super.clone(); // no deep copy necessary
+    }
   }
 
   /**
@@ -217,5 +222,10 @@ public ClassNode(String display, String clsname) {
     public String getClassName() {
       return clsname;
     }
+
+    @Override
+    public Object clone() {
+      return super.clone(); // no deep copy necessary
+    }
   }
 }
diff --git a/...ex-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java b/...ex-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTree.java
@@ -23,6 +23,10 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import elki.database.datastore.DataStore;
+import elki.database.datastore.DataStoreFactory;
+import elki.database.datastore.DataStoreUtil;
+import elki.database.datastore.WritableDataStore;
 import elki.database.ids.*;
 import elki.database.query.distance.DistanceQuery;
 import elki.database.query.knn.KNNSearcher;
@@ -105,11 +109,10 @@ public double distance(DBIDRef id1, DBIDRef id2) {
    * @deprecated Change to use by-object NN lookups instead.
    */
   @Deprecated
-  protected final Map<DBID, KNNList> batchNN(N node, DBIDs ids, int kmax) {
-    Map<DBID, KNNList> res = new HashMap<>(ids.size());
+  protected final DataStore<KNNList> batchNN(N node, DBIDs ids, int kmax) {
+    WritableDataStore<KNNList> res = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_TEMP, KNNList.class);
     for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
-      DBID id = DBIDUtil.deref(iter);
-      res.put(id, knnq.getKNN(id, kmax));
+      res.put(iter, knnq.getKNN(iter, kmax));
     }
     return res;
   }

diff --git a/...e/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java b/...e/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/AbstractMkTreeUnified.java
@@ -21,9 +21,8 @@
 package elki.index.tree.metrical.mtreevariants.mktrees;
 
 import java.util.List;
-import java.util.Map;
 
-import elki.database.ids.DBID;
+import elki.database.datastore.DataStore;
 import elki.database.ids.DBIDUtil;
 import elki.database.ids.KNNList;
 import elki.database.ids.ModifiableDBIDs;
@@ -86,7 +85,7 @@ public void insertAll(List<E> entries) {
       super.insert(entry, false);
     }
 
-    Map<DBID, KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax);
+    DataStore<KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax);
     kNNdistanceAdjustment(getRootEntry(), knnLists);
     doExtraIntegrityChecks();
   }
@@ -97,7 +96,7 @@ public void insertAll(List<E> entries) {
    * @param entry the root entry of the current subtree
    * @param knnLists a map of knn lists for each leaf entry
    */
-  protected abstract void kNNdistanceAdjustment(E entry, Map<DBID, KNNList> knnLists);
+  protected abstract void kNNdistanceAdjustment(E entry, DataStore<KNNList> knnLists);
 
   /**
    * Get the value of k_max.

diff --git a/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java b/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTree.java
@@ -21,19 +21,9 @@
 package elki.index.tree.metrical.mtreevariants.mktrees.mkapp;
 
 import java.util.List;
-import java.util.Map;
-
-import elki.database.ids.ArrayModifiableDBIDs;
-import elki.database.ids.DBID;
-import elki.database.ids.DBIDIter;
-import elki.database.ids.DBIDRef;
-import elki.database.ids.DBIDUtil;
-import elki.database.ids.DBIDs;
-import elki.database.ids.DoubleDBIDList;
-import elki.database.ids.DoubleDBIDListIter;
-import elki.database.ids.KNNList;
-import elki.database.ids.ModifiableDBIDs;
-import elki.database.ids.ModifiableDoubleDBIDList;
+
+import elki.database.datastore.DataStore;
+import elki.database.ids.*;
 import elki.database.relation.Relation;
 import elki.index.tree.LeafEntry;
 import elki.index.tree.metrical.mtreevariants.mktrees.AbstractMkTree;
@@ -45,6 +35,7 @@
 import elki.utilities.datastructures.heap.Heap;
 import elki.utilities.datastructures.heap.UpdatableHeap;
 import elki.utilities.io.ByteArrayUtil;
+
 import net.jafama.FastMath;
 
 /**
@@ -120,7 +111,7 @@ public void insertAll(List<MkAppEntry> entries) {
       super.insert(entry, false);
     }
 
-    Map<DBID, KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax + 1);
+    DataStore<KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax + 1);
 
     adjustApproximatedKNNDistances(getRootEntry(), knnLists);
     doExtraIntegrityChecks();
@@ -246,7 +237,7 @@ protected void initializeCapacities(MkAppEntry exampleLeaf) {
    * @param knnLists kNN lists
    * @return Mean kNN values
    */
-  private double[] getMeanKNNList(DBIDs ids, Map<DBID, KNNList> knnLists) {
+  private double[] getMeanKNNList(DBIDs ids, DataStore<KNNList> knnLists) {
     double[] means = new double[settings.kmax];
     for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
       KNNList knns = knnLists.get(iter);
@@ -264,7 +255,7 @@ private double[] getMeanKNNList(DBIDs ids, Map<DBID, KNNList> knnLists) {
    * @param entry the root entry of the current subtree
    * @param knnLists a map of knn lists for each leaf entry
    */
-  private void adjustApproximatedKNNDistances(MkAppEntry entry, Map<DBID, KNNList> knnLists) {
+  private void adjustApproximatedKNNDistances(MkAppEntry entry, DataStore<KNNList> knnLists) {
     MkAppTreeNode<O> node = getNode(entry);
 
     if(node.isLeaf()) {

diff --git a/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java b/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkcop/MkCoPTree.java
@@ -22,17 +22,9 @@
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
-
-import elki.database.ids.DBID;
-import elki.database.ids.DBIDIter;
-import elki.database.ids.DBIDRef;
-import elki.database.ids.DBIDUtil;
-import elki.database.ids.DoubleDBIDList;
-import elki.database.ids.DoubleDBIDListIter;
-import elki.database.ids.KNNList;
-import elki.database.ids.ModifiableDBIDs;
-import elki.database.ids.ModifiableDoubleDBIDList;
+
+import elki.database.datastore.DataStore;
+import elki.database.ids.*;
 import elki.database.relation.Relation;
 import elki.index.tree.metrical.mtreevariants.mktrees.AbstractMkTree;
 import elki.index.tree.metrical.mtreevariants.mktrees.MkTreeSettings;
@@ -43,7 +35,6 @@
 import elki.utilities.exceptions.AbortException;
 import elki.utilities.io.ByteArrayUtil;
 import elki.utilities.io.FormatUtil;
-import net.jafama.FastMath;
 
 /**
  * MkCopTree is a metrical index structure based on the concepts of the M-Tree
@@ -122,7 +113,7 @@ public void insertAll(List<MkCoPEntry> entries) {
       super.insert(entry, false);
     }
 
-    Map<DBID, KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax);
+    DataStore<KNNList> knnLists = batchNN(getNode(getRootID()), ids, settings.kmax);
 
     adjustApproximatedKNNDistances(getRootEntry(), knnLists);
     doExtraIntegrityChecks();
@@ -147,7 +138,7 @@ public DoubleDBIDList reverseKNNQuery(DBIDRef id, int k) {
     doReverseKNNQuery(k, id, result, candidates);
 
     // refinement of candidates
-    Map<DBID, KNNList> knnLists = batchNN(getNode(getRootID()), candidates, k);
+    DataStore<KNNList> knnLists = batchNN(getNode(getRootID()), candidates, k);
 
     result.sort();
     // Collections.sort(candidates);
@@ -157,11 +148,10 @@ public DoubleDBIDList reverseKNNQuery(DBIDRef id, int k) {
     // rkNNStatistics.addTrueHits(result.size());
 
     for(DBIDIter iter = candidates.iter(); iter.valid(); iter.advance()) {
-      DBID cid = DBIDUtil.deref(iter);
-      KNNList cands = knnLists.get(cid);
+      KNNList cands = knnLists.get(iter);
       for(DoubleDBIDListIter iter2 = cands.iter(); iter2.valid(); iter2.advance()) {
         if(DBIDUtil.equal(id, iter2)) {
-          result.add(iter2.doubleValue(), cid);
+          result.add(iter2.doubleValue(), iter);
           break;
         }
       }
@@ -290,9 +280,8 @@ private void doReverseKNNQuery(int k, DBIDRef q, ModifiableDoubleDBIDList result
    * @param entry the root entry of the current subtree
    * @param knnLists a map of knn lists for each leaf entry
    */
-  private void adjustApproximatedKNNDistances(MkCoPEntry entry, Map<DBID, KNNList> knnLists) {
+  private void adjustApproximatedKNNDistances(MkCoPEntry entry, DataStore<KNNList> knnLists) {
     MkCoPTreeNode<O> node = getNode(entry);
-
     if(node.isLeaf()) {
       for(int i = 0; i < node.getNumEntries(); i++) {
         MkCoPLeafEntry leafEntry = (MkCoPLeafEntry) node.getEntry(i);
@@ -305,7 +294,6 @@ private void adjustApproximatedKNNDistances(MkCoPEntry entry, Map<DBID, KNNList>
         adjustApproximatedKNNDistances(dirEntry, knnLists);
       }
     }
-
     ApproximationLine approx = node.conservativeKnnDistanceApproximation(settings.kmax);
     entry.setConservativeKnnDistanceApproximation(approx);
   }

diff --git a/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java b/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mkmax/MkMaxTree.java
@@ -21,18 +21,9 @@
 package elki.index.tree.metrical.mtreevariants.mktrees.mkmax;
 
 import java.util.List;
-import java.util.Map;
-
-import elki.database.ids.DBID;
-import elki.database.ids.DBIDIter;
-import elki.database.ids.DBIDRef;
-import elki.database.ids.DBIDUtil;
-import elki.database.ids.DoubleDBIDList;
-import elki.database.ids.DoubleDBIDListIter;
-import elki.database.ids.KNNHeap;
-import elki.database.ids.KNNList;
-import elki.database.ids.ModifiableDBIDs;
-import elki.database.ids.ModifiableDoubleDBIDList;
+
+import elki.database.datastore.DataStore;
+import elki.database.ids.*;
 import elki.database.relation.Relation;
 import elki.index.tree.metrical.mtreevariants.mktrees.AbstractMkTreeUnified;
 import elki.index.tree.metrical.mtreevariants.mktrees.MkTreeSettings;
@@ -99,15 +90,14 @@ public DoubleDBIDList reverseKNNQuery(DBIDRef id, int k) {
     for (DBIDIter candidate = candidates.iter(); candidate.valid(); candidate.advance()) {
       candidateIDs.add(candidate);
     }
-    Map<DBID, KNNList> knnLists = batchNN(getNode(getRootID()), candidateIDs, k);
+    DataStore<KNNList> knnLists = batchNN(getNode(getRootID()), candidateIDs, k);
 
     ModifiableDoubleDBIDList result = DBIDUtil.newDistanceDBIDList();
     for (DBIDIter iter = candidateIDs.iter(); iter.valid(); iter.advance()) {
-      DBID cid = DBIDUtil.deref(iter);
-      KNNList cands = knnLists.get(cid);
+      KNNList cands = knnLists.get(iter);
       for (DoubleDBIDListIter iter2 = cands.iter(); iter2.valid(); iter2.advance()) {
         if (DBIDUtil.equal(id, iter2)) {
-          result.add(iter2.doubleValue(), cid);
+          result.add(iter2.doubleValue(), iter);
           break;
         }
       }
@@ -134,7 +124,7 @@ protected void preInsert(MkMaxEntry entry) {
    * Adjusts the knn distance in the subtree of the specified root entry.
    */
   @Override
-  protected void kNNdistanceAdjustment(MkMaxEntry entry, Map<DBID, KNNList> knnLists) {
+  protected void kNNdistanceAdjustment(MkMaxEntry entry, DataStore<KNNList> knnLists) {
     MkMaxTreeNode<O> node = getNode(entry);
     double knnDist_node = 0.;
     if (node.isLeaf()) {

diff --git a/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java b/...x-mtree/src/main/java/elki/index/tree/metrical/mtreevariants/mktrees/mktab/MkTabTree.java
@@ -20,15 +20,8 @@
  */
 package elki.index.tree.metrical.mtreevariants.mktrees.mktab;
 
-import java.util.Map;
-
-import elki.database.ids.DBID;
-import elki.database.ids.DBIDRef;
-import elki.database.ids.DBIDUtil;
-import elki.database.ids.DoubleDBIDList;
-import elki.database.ids.DoubleDBIDListIter;
-import elki.database.ids.KNNList;
-import elki.database.ids.ModifiableDoubleDBIDList;
+import elki.database.datastore.DataStore;
+import elki.database.ids.*;
 import elki.database.relation.Relation;
 import elki.index.tree.metrical.mtreevariants.mktrees.AbstractMkTreeUnified;
 import elki.index.tree.metrical.mtreevariants.mktrees.MkTreeSettings;
@@ -131,7 +124,7 @@ protected void initializeCapacities(MkTabEntry exampleLeaf) {
   }
 
   @Override
-  protected void kNNdistanceAdjustment(MkTabEntry entry, Map<DBID, KNNList> knnLists) {
+  protected void kNNdistanceAdjustment(MkTabEntry entry, DataStore<KNNList> knnLists) {
     MkTabTreeNode<O> node = getNode(entry);
     double[] knnDistances_node = initKnnDistanceList();
     if(node.isLeaf()) {