Incorporate epsilon in to log transform

Issue #332 In some cases, log being calculated without catching zeros. Incorporate e;silon into log transform.

src/AudioAnalysisTools/DSP/DSP_Filters.cs

@@ -88,6 +88,7 @@ public static void TestMethod_GenerateSignal2()
             var freqScale = new FrequencyScale(FreqScaleType.OctaveCustom, nyquist, frameSize, linearBound, octaveToneCount, gridInterval);
             string path = @"C:\SensorNetworks\Output\Sonograms\UnitTestSonograms\SineSignal2.png";
             var recording = GenerateTestRecording(sampleRate, duration, harmonics, WaveType.Cosine);
+            var epsilon = recording.Epsilon;
 
             // init the default sonogram config
             var sonoConfig = new SonogramConfig
@@ -98,8 +99,9 @@ public static void TestMethod_GenerateSignal2()
                 NoiseReductionType = NoiseReductionType.None,
                 NoiseReductionParameter = 0.0,
             };
+
             var sonogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
-            sonogram.Data = OctaveFreqScale.ConvertAmplitudeSpectrogramToDecibelOctaveScale(sonogram.Data, freqScale);
+            sonogram.Data = OctaveFreqScale.ConvertAmplitudeSpectrogramToDecibelOctaveScale(sonogram.Data, freqScale, epsilon);
 
             // pick a row, any row
             var oneSpectrum = MatrixTools.GetRow(sonogram.Data, 40);

src/AudioAnalysisTools/Indices/IndexMatrices.cs

@@ -395,7 +395,8 @@ public static Dictionary<string, double[]> AddDerivedIndices(Dictionary<string,
             summaryIndices.Add("SqrtTempEntropy", DataTools.SquareRootOfValues(summaryIndices["TemporalEntropy"]));
 
             // insert some transformed data columns
-            summaryIndices.Add("LogTempEntropy", DataTools.LogTransform(summaryIndices["TemporalEntropy"]));
+            var epsilon = Acoustics.Tools.Wav.WavReader.CalculateEpsilonForRescaledInteger(16);
+            summaryIndices.Add("LogTempEntropy", DataTools.Log10Values(summaryIndices["TemporalEntropy"], epsilon));
 
             // Calculate Normalised Difference Soundscape Index if not already done
             // caluclate two ratios for three bands.  DO NOT CHANGE THESE KEYS

src/TowseyLibrary/DataTools.cs

@@ -1278,7 +1278,7 @@ public static int[] Peaks_CropToFirstAndLast(double[] data, double severity)
         }
 
         /// <summary>
-        /// Finds the local peaks in a vector.
+        /// Finds the local maxima in a vector.
         /// </summary>
         public static bool[] GetPeaks(double[] data)
         {
@@ -2961,38 +2961,6 @@ public static double DotProduct(double[,] m1, double[,] m2)
             return sum;
         }
 
-        /// <summary>
-        /// convert values to Decibels.
-        /// Assume that all values are positive.
-        /// </summary>
-        /// <param name="m">matrix of positive power values.</param>
-        public static double[,] DeciBels(double[,] m, out double min, out double max)
-        {
-            min = double.MaxValue;
-            max = -double.MaxValue;
-
-            int rows = m.GetLength(0);
-            int cols = m.GetLength(1);
-            double[,] ret = new double[rows, cols];
-
-            for (int i = 0; i < rows; i++)
-            {
-                for (int j = 0; j < cols; j++)
-                {
-                    double dBels = 10 * Math.Log10(m[i, j]);    // convert power to decibels
-
-                    // NOTE: the decibels calculation should be a ratio.
-                    // Here the ratio is implied ie relative to the power in the original normalised signal
-                    //        if (dBels <= min) min = dBels;
-                    //      else
-                    //    if (dBels >= max) max = dBels;
-                    ret[i, j] = dBels;
-                }
-            }
-
-            return ret;
-        }
-
         public static double[] Order(double[] array, double[] order)
         {
             int length = array.Length;
@@ -3254,8 +3222,10 @@ public static double[] NormaliseValues(int[] val, int normMin, int normMax)
         }
 
         /// <summary>
-        /// normalizes the passed array between 0,1.
+        /// Normalizes the passed array between 0,1.
         /// Ensures all values are positive.
+        /// Minimum array value set = 0.0.
+        /// Maximum array value set = 1.0.
         /// </summary>
         public static double[] normalise(double[] v)
         {
@@ -3676,30 +3646,13 @@ public static double[] SquareRootOfValues(double[] data)
             return sqrtArray;
         }
 
-        public static double[] LogTransform(double[] data)
-        {
-            if (data == null)
-            {
-                return null;
-            }
-
-            var logArray = new double[data.Length];
-            for (int i = 0; i < data.Length; i++)
-            {
-                if (data[i] <= 0.0)
-                {
-                    logArray[i] = 0.0;
-                }
-                else
-                {
-                    logArray[i] = Math.Log10(1 + data[i]);
-                }
-            }
-
-            return logArray;
-        }
-
-        public static double[] LogValues(double[] data)
+        /// <summary>
+        /// Gets the log10 of an array of values.
+        /// Assume that all values are non-zero and positive.
+        /// </summary>
+        /// <param name="data">The input data array.</param>
+        /// <param name="epsilon">The smallest accepted non-zero value.</param>
+        public static double[] Log10Values(double[] data, double epsilon)
         {
             if (data == null)
             {
@@ -3709,9 +3662,9 @@ public static double[] LogValues(double[] data)
             var logArray = new double[data.Length];
             for (int i = 0; i < data.Length; i++)
             {
-                if (data[i] <= 0.0)
+                if (data[i] <= epsilon)
                 {
-                    logArray[i] = -1000000.0;
+                    logArray[i] = Math.Log10(epsilon);
                 }
                 else
                 {

src/TowseyLibrary/MatrixTools.cs

@@ -522,11 +522,13 @@ public static double[] Matrix2Array(double[,] matrix)
         /// Convert the power values in a matrix of spectrogram values to Decibels.
         /// Assume that all matrix values are positive i.e. due to prior noise removal.
         /// NOTE: This method also returns the min and max decibel values in the passed matrix.
+        /// NOTE: A decibel value should be a ratio.
+        ///       Here the ratio is implied ie it is relative to the value of maximum power in the original normalised signal.
         /// </summary>
         /// <param name="m">matrix of positive power values.</param>
         /// <param name="min">min value to be return by out.</param>
         /// <param name="max">max value to be return by out.</param>
-        public static double[,] Power2DeciBels(double[,] m, out double min, out double max)
+        public static double[,] Power2DeciBels(double[,] m, double epsilon, out double min, out double max)
         {
             min = double.MaxValue;
             max = -double.MaxValue;
@@ -539,16 +541,18 @@ public static double[] Matrix2Array(double[,] matrix)
             {
                 for (int j = 0; j < cols; j++)
                 {
-                    double dBels = 10 * Math.Log10(m[i, j]); //convert power to decibels
+                    double dBels = 10 * Math.Log10(epsilon); //convert power to decibels
+                    if (m[i, j] > epsilon)
+                    {
+                        dBels = 10 * Math.Log10(m[i, j]); //convert power to decibels
+                    }
 
-                    //NOTE: the decibel calculation should be a ratio.
-                    // Here the ratio is implied ie relative to the power in the original normalised signal
-                    if (dBels <= min)
+                    if (dBels < min)
                     {
                         min = dBels;
                     }
                     else
-                    if (dBels >= max)
+                    if (dBels > max)
                     {
                         max = dBels;
                     }