BigInteger is too slow use double instead

Also replaced Math.Log(x, 2) with Math.Log2(x)
intervals-mining-lab · Jan 21, 2025 · b0f664e · b0f664e
1 parent a39b563
commit b0f664e
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Showing 19 changed files with 27 additions and 26 deletions.
diff --git a/Libiada.Core/Core/Characteristics/Calculators/BinaryCalculators/GeometricMean.cs b/Libiada.Core/Core/Characteristics/Calculators/BinaryCalculators/GeometricMean.cs
@@ -29,7 +29,7 @@ public override double Calculate(BinaryIntervalsManager manager, Link link)
 
         int[] intervals = manager.GetIntervals();
 
-        double result = intervals.Where(t => t > 0).Sum(t => Math.Log(t, 2));
+        double result = intervals.Where(t => t > 0).Sum(t => Math.Log2(t));
 
         return intervals.Length == 0 ? 0 : Math.Pow(2, result / intervals.Length);
     }

diff --git a/Libiada.Core/Core/Characteristics/Calculators/BinaryCalculators/Redundancy.cs b/Libiada.Core/Core/Characteristics/Calculators/BinaryCalculators/Redundancy.cs
@@ -41,21 +41,21 @@ public override double Calculate(BinaryIntervalsManager manager, Link link)
                     currentEntrance = manager.GetFirstAfter(manager.GetFirst(i));
                     if (link == Link.Start || link == Link.Both)
                     {
-                        avG += Math.Log(currentEntrance, 2);
+                        avG += Math.Log2(currentEntrance);
                     }
                 }
                 else
                 {
                     int nextEntrance = manager.GetFirstAfter(manager.GetFirst(i));
-                    avG += Math.Log(nextEntrance - currentEntrance, 2);
+                    avG += Math.Log2(nextEntrance - currentEntrance);
                     currentEntrance = nextEntrance;
                 }
             }
         }
 
         if (link == Link.End || link == Link.Both)
         {
-            avG += Math.Log(manager.Length - currentEntrance, 2);
+            avG += Math.Log2(manager.Length - currentEntrance);
         }
 
         avG = manager.PairsCount == 0 ? 0 : avG / manager.PairsCount;

diff --git a/.../Core/Characteristics/Calculators/CongenericCalculators/CuttingLengthVocabularyEntropy.cs b/.../Core/Characteristics/Calculators/CongenericCalculators/CuttingLengthVocabularyEntropy.cs
@@ -18,7 +18,7 @@ public override double Calculate(CongenericSequence sequence)
     {
         double cuttingLength = new CuttingLength().Calculate(sequence);
 
-        return Math.Log(sequence.Length - cuttingLength + 1, 2);
+        return Math.Log2(sequence.Length - cuttingLength + 1);
     }
 
 }
diff --git a/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/Depth.cs b/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/Depth.cs
@@ -26,9 +26,9 @@ public double Calculate(CongenericSequence sequence, Link link)
         int[] intervals = sequence.GetArrangement(link);
         if(intervals.Length == 0) return 0;
 
-        BigInteger volume = 1;
-        foreach(int interval in intervals) volume *= interval;
+        double depth = 0;
+        foreach(int interval in intervals) depth += Math.Log2(interval);
 
-        return BigInteger.Log(volume, 2);
+        return depth;
     }
 }
diff --git a/...ada.Core/Core/Characteristics/Calculators/CongenericCalculators/IdentifyingInformation.cs b/...ada.Core/Core/Characteristics/Calculators/CongenericCalculators/IdentifyingInformation.cs
@@ -27,6 +27,6 @@ public double Calculate(CongenericSequence sequence, Link link)
     {
         double mean = new ArithmeticMean().Calculate(sequence, link);
 
-        return mean == 0 ? 0 : Math.Log(mean, 2);
+        return mean == 0 ? 0 : Math.Log2(mean);
     }
 }
diff --git a/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessKurtosis.cs b/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessKurtosis.cs
@@ -33,7 +33,7 @@ public double Calculate(CongenericSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - gDeltaLog;
+            double centeredRemoteness = Math.Log2(interval) - gDeltaLog;
             result += centeredRemoteness * centeredRemoteness * centeredRemoteness * centeredRemoteness * nk / nj;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessSkewness.cs b/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessSkewness.cs
@@ -33,7 +33,7 @@ public double Calculate(CongenericSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - gDeltaLog;
+            double centeredRemoteness = Math.Log2(interval) - gDeltaLog;
             result += centeredRemoteness * centeredRemoteness * centeredRemoteness * nk / nj;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessVariance.cs b/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/RemotenessVariance.cs
@@ -33,7 +33,7 @@ public double Calculate(CongenericSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - gDeltaLog;
+            double centeredRemoteness = Math.Log2(interval) - gDeltaLog;
             result += centeredRemoteness * centeredRemoteness * nk / nj;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/Volume.cs b/Libiada.Core/Core/Characteristics/Calculators/CongenericCalculators/Volume.cs
@@ -1,7 +1,5 @@
 namespace Libiada.Core.Core.Characteristics.Calculators.CongenericCalculators;
 
-using System.Numerics;
-
 /// <summary>
 /// Volume of sequence.
 /// </summary>
@@ -24,9 +22,9 @@ public double Calculate(CongenericSequence sequence, Link link)
         int[] intervals = sequence.GetArrangement(link);
         if (intervals.Length == 0) return 1;
 
-        BigInteger result = 1;
+        double result = 1;
         foreach (int interval in intervals) result *= interval;
 
-        return (double)result;
+        return result;
     }
 }
diff --git a/...a.Core/Core/Characteristics/Calculators/FullCalculators/CuttingLengthVocabularyEntropy.cs b/...a.Core/Core/Characteristics/Calculators/FullCalculators/CuttingLengthVocabularyEntropy.cs
@@ -17,6 +17,6 @@ public class CuttingLengthVocabularyEntropy : NonLinkableFullCalculator
     public override double Calculate(ComposedSequence sequence)
     {
         double cutLength = new CuttingLength().Calculate(sequence);
-        return Math.Log(sequence.Length - cutLength + 1, 2);
+        return Math.Log2(sequence.Length - cutLength + 1);
     }
 }
diff --git a/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosis.cs b/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosis.cs
@@ -39,7 +39,7 @@ public double Calculate(ComposedSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - g;
+            double centeredRemoteness = Math.Log2(interval) - g;
             result += centeredRemoteness * centeredRemoteness * centeredRemoteness * centeredRemoteness * nk / n;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewness.cs b/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewness.cs
@@ -39,7 +39,7 @@ public double Calculate(ComposedSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - g;
+            double centeredRemoteness = Math.Log2(interval) - g;
             result += centeredRemoteness * centeredRemoteness * centeredRemoteness * nk / n;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessVariance.cs b/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/RemotenessVariance.cs
@@ -39,7 +39,7 @@ public double Calculate(ComposedSequence sequence, Link link)
 
         foreach ((int interval, int nk) in intervalsDictionary)
         {
-            double centeredRemoteness = Math.Log(interval, 2) - g;
+            double centeredRemoteness = Math.Log2(interval) - g;
             result += centeredRemoteness * centeredRemoteness * nk / n;
         }
 

diff --git a/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/VariationsCount.cs b/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/VariationsCount.cs
@@ -1,7 +1,6 @@
 namespace Libiada.Core.Core.Characteristics.Calculators.FullCalculators;
 
 using Libiada.Core.Core.SimpleTypes;
-using System.Numerics;
 
 /// <summary>
 /// Count of probable sequences that can be generated
@@ -20,7 +19,7 @@ public class VariationsCount : NonLinkableFullCalculator
     /// </returns>
     public override double Calculate(ComposedSequence sequence)
     {
-        BigInteger count = 1;
+        double count = 1;
         for (int i = 0; i < sequence.Length; i++)
         {
             if (sequence[i] is ValuePhantom message)

diff --git a/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/Volume.cs b/Libiada.Core/Core/Characteristics/Calculators/FullCalculators/Volume.cs
@@ -1,7 +1,5 @@
 namespace Libiada.Core.Core.Characteristics.Calculators.FullCalculators;
 
-using System.Numerics;
-
 /// <summary>
 /// Volume of sequence.
 /// </summary>
@@ -23,11 +21,11 @@ public double Calculate(ComposedSequence sequence, Link link)
     {
         CongenericCalculators.Volume calculator = new();
 
-        BigInteger result = 1;
+        double result = 1;
         int alphabetCardinality = sequence.Alphabet.Cardinality;
         for (int i = 0; i < alphabetCardinality; i++)
         {
-            result *= (BigInteger)calculator.Calculate(sequence.CongenericSequence(i), link);
+            result *= calculator.Calculate(sequence.CongenericSequence(i), link);
         }
 
         return (double)result;

diff --git a/Libiada.Segmenter/Model/Criterion/CriterionMinSymmetryByIntervals.cs b/Libiada.Segmenter/Model/Criterion/CriterionMinSymmetryByIntervals.cs
@@ -42,6 +42,7 @@ public double GetTaxonsValue(FrequencyDictionary alphabet)
         for (int index = 0; index < alphabet.Count; index++)
         {
             int countT = positions[index].Count;
+            // TODO: check if this should be Log2
             taxons += (Math.Log(countT) * countT) - countT;
         }
 

diff --git a/Libiada.Segmenter/Model/Criterion/CriterionMinSymmetryByShrader.cs b/Libiada.Segmenter/Model/Criterion/CriterionMinSymmetryByShrader.cs
@@ -87,6 +87,7 @@ private double Symmetry(FrequencyDictionary alphabet)
         for (int index = 0; index < alphabet.Count; index++)
         {
             int countT = positions[index].Count;
+            // TODO: check if this should be Log2
             taxons += (Math.Log(countT) * countT) - countT;
             int arraySize = positions[index].Count;
             if (arrayMaxLength < arraySize)
@@ -105,6 +106,7 @@ private double Symmetry(FrequencyDictionary alphabet)
                 }
             }
 
+            // TODO: check if this should be Log2
             merons += (Math.Log(countM) * countM) - countM;
             countM = 0;
         }

diff --git a/Libiada.Segmenter/Model/Criterion/CriterionPartialOrlov.cs b/Libiada.Segmenter/Model/Criterion/CriterionPartialOrlov.cs
@@ -88,6 +88,7 @@ public double TheoryVolume(ComplexSequence sequence, FrequencyDictionary alphabe
         }
 
         double z = sequence.Length;
+        // TODO: check if this should be Log2
         double k = 1 / Math.Log(f * z);
         double b = (k / f) - 1;
         double v = (k * z) - b;
@@ -145,6 +146,7 @@ public double CalculateB(double k, double f1)
     /// </returns>
     public double CalculateK(int factFrequency, int length)
     {
+        // TODO: check if this should be Log2
         return 1.0 / Math.Log(factFrequency * length);
     }
 

diff --git a/Libiada.Segmenter/PoemsSegmenter/PartialOrlovCriterion.cs b/Libiada.Segmenter/PoemsSegmenter/PartialOrlovCriterion.cs
@@ -33,6 +33,7 @@ public double CalculateK()
         double maxEntriesNumber = consonancesDictionary.Values.Max();
         double Z = calculateZ();
         string textWithoutSpaces = text.Replace(" ", "");
+        // TODO: check if this should be Log2
         return 1 / Math.Log(maxEntriesNumber);
     }