Create new class to contain DCT methods

Issue #500 Create a new class  to contain DCT methods. Shift across methods from MFCCStuff.cs. Make this a static class but it could/should eventually be used to contain the parameters required to perform the DCT.

A bunch of other methods where affected by this shift of DCT methods.

src/AnalysisPrograms/Recognizers/Frogs/LitoriaBicolor.cs

@@ -193,7 +193,7 @@ public static Tuple<BaseSonogram, double[,], double[], List<AcousticEvent>, Imag
             int dctLength = (int)Math.Round(framesPerSecond * dctDuration);
 
             // set up the cosine coefficients
-            double[,] cosines = MFCCStuff.Cosines(dctLength, dctLength);
+            double[,] cosines = DctMethods.Cosines(dctLength, dctLength);
 
             int upperBandMinBin = (int)Math.Round(lbConfig.UpperBandMinHz / freqBinWidth) + 1;
             int upperBandMaxBin = (int)Math.Round(lbConfig.UpperBandMaxHz / freqBinWidth) + 1;

src/AnalysisPrograms/Recognizers/Frogs/LitoriaRothii.cs

@@ -136,7 +136,7 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
             int dctLength = (int)Math.Round(framesPerSecond * dctDuration);
 
             // set up the cosine coefficients
-            double[,] cosines = MFCCStuff.Cosines(dctLength, dctLength);
+            double[,] cosines = DctMethods.Cosines(dctLength, dctLength);
 
             BaseSonogram sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
             int rowCount = sonogram.Data.GetLength(0);

src/AudioAnalysisTools/DSP/DctMethods.cs

@@ -0,0 +1,74 @@
+// <copyright file="DctMethods.cs" company="QutEcoacoustics">
+// All code in this file and all associated files are the copyright and property of the QUT Ecoacoustics Research Group (formerly MQUTeR, and formerly QUT Bioacoustics Research Group).
+// </copyright>
+
+namespace AudioAnalysisTools.DSP
+{
+    using System;
+    using System.Collections.Generic;
+    using System.Linq;
+    using System.Text;
+    using System.Threading.Tasks;
+    using TowseyLibrary;
+
+    public static class DctMethods
+    {
+        /// <summary>
+        /// Returns a matrix of cosine basis functions.
+        /// These are prepared prior to performing a DCT, Discrete Cosine Transform.
+        /// The rows k = 0 to coeffCount are the basis functions.
+        /// The columns, m = 0 to M where M = signalLength or the length of the required DCT.
+        /// The value of m/M ranges from 0 to 1.0.
+        /// The value of Pi*m/M ranges from 0 to Pi radians.
+        /// The value of k*Pi*m/M ranges from 0 to k*Pi radians. WHen k=2, 2Pi radians corresponds to one rotation.
+        /// </summary>
+        /// <param name="signalLength">The length of the signal to be processed. e.g. the frequency bin count or filter bank count or ...</param>
+        /// <param name="coeffCount">The number of basis funcitons = the rquired number of DCT coefficients.</param>
+        public static double[,] Cosines(int signalLength, int coeffCount)
+        {
+            double[,] cosines = new double[coeffCount + 1, signalLength]; //get an extra coefficient because do not want DC coeff at [0].
+            for (int k = 0; k < coeffCount + 1; k++)
+            {
+                double kPiOnM = k * Math.PI / signalLength;
+
+                // for each spectral bin
+                for (int m = 0; m < signalLength; m++)
+                {
+                    cosines[k, m] = Math.Cos(kPiOnM * (m + 0.5)); //can also be Cos(kPiOnM * (m - 0.5)
+                }
+            }
+
+            return cosines;
+        }
+
+        //following two lines write matrix of cos values for checking.
+        //string fPath = @"C:\SensorNetworks\Sonograms\cosines.txt";
+        //FileTools.WriteMatrix2File_Formatted(cosines, fPath, "F3");
+
+        //following two lines write bmp image of cos values for checking.
+        //string fPath = @"C:\SensorNetworks\Output\cosines.bmp";
+        //ImageTools.DrawMatrix(cosines, fPath);
+
+        public static double[] DoDct(double[] vector, double[,] cosines, int lowerDctBound)
+        {
+            var dctArray = DataTools.SubtractMean(vector);
+            int dctLength = dctArray.Length;
+            double[] dctCoeff = MFCCStuff.CalculateCeptrum(dctArray, cosines);
+
+            // convert to absolute values because not interested in negative values due to phase.
+            for (int i = 0; i < dctLength; i++)
+            {
+                dctCoeff[i] = Math.Abs(dctCoeff[i]);
+            }
+
+            // remove lower coefficients from consideration because they dominate
+            for (int i = 0; i < lowerDctBound; i++)
+            {
+                dctCoeff[i] = 0.0;
+            }
+
+            dctCoeff = DataTools.normalise2UnitLength(dctCoeff);
+            return dctCoeff;
+        }
+    }
+}

src/AudioAnalysisTools/DSP/MFCCStuff.cs

@@ -477,21 +477,13 @@ public static double InverseHerzTranform(double m, double c, double div)
             int binCount = spectra.GetLength(1);  //number of filters in filter bank
 
             //set up the cosine coefficients. Need one extra to compensate for DC coeff.
-            double[,] cosines = Cosines(binCount, coeffCount + 1);
-
-            //following two lines write matrix of cos values for checking.
-            //string fPath = @"path\cosines.txt";
-            //FileTools.WriteMatrix2File_Formatted(cosines, fPath, "F3");
-
-            //following two lines write bmp image of cos values for checking.
-            //string fPath = @"path\cosines.bmp";
-            //ImageTools.DrawMatrix(cosines, fPath);
+            double[,] cosines = DctMethods.Cosines(binCount, coeffCount + 1);
 
             double[,] op = new double[frameCount, coeffCount];
             for (int i = 0; i < frameCount; i++)
             {
                 double[] spectrum = DataTools.GetRow(spectra, i); //transfer matrix row=i to vector
-                double[] cepstrum = DCT(spectrum, cosines);
+                double[] cepstrum = CalculateCeptrum(spectrum, cosines);
 
                 for (int j = 0; j < coeffCount; j++)
                 {
@@ -512,7 +504,7 @@ public static double InverseHerzTranform(double m, double c, double div)
             for (int i = 0; i < frameCount; i++)
             {
                 double[] spectrum = DataTools.GetRow(spectra, i); //transfer matrix row=i to vector
-                double[] cepstrum = DCT(spectrum, cosines);
+                double[] cepstrum = CalculateCeptrum(spectrum, cosines);
 
                 for (int j = 0; j < coeffCount; j++)
                 {
@@ -523,35 +515,7 @@ public static double InverseHerzTranform(double m, double c, double div)
             return op;
         }
 
-        /// <summary>
-        /// Returns a matrix of cosine basis functions.
-        /// These are prepared prior to performing a DCT, Discrete Cosine Transform.
-        /// The rows k = 0 to coeffCount are the basis functions.
-        /// The columns, m = 0 to M where M = signalLength or the length of the required DCT.
-        /// The value of m/M ranges from 0 to 1.0.
-        /// The value of Pi*m/M ranges from 0 to Pi radians.
-        /// The value of k*Pi*m/M ranges from 0 to k*Pi radians. WHen k=2, 2Pi radians corresponds to one rotation.
-        /// </summary>
-        /// <param name="signalLength">The length of the signal to be processed. e.g. the frequency bin count or filter bank count or ...</param>
-        /// <param name="coeffCount">The number of basis funcitons = the rquired number of DCT coefficients.</param>
-        public static double[,] Cosines(int signalLength, int coeffCount)
-        {
-            double[,] cosines = new double[coeffCount + 1, signalLength]; //get an extra coefficient because do not want DC coeff at [0].
-            for (int k = 0; k < coeffCount + 1; k++)
-            {
-                double kPiOnM = k * Math.PI / signalLength;
-
-                // for each spectral bin
-                for (int m = 0; m < signalLength; m++)
-                {
-                    cosines[k, m] = Math.Cos(kPiOnM * (m + 0.5)); //can also be Cos(kPiOnM * (m - 0.5)
-                }
-            }
-
-            return cosines;
-        }
-
-        public static double[] DCT(double[] spectrum, double[,] cosines)
+        public static double[] CalculateCeptrum(double[] spectrum, double[,] cosines)
         {
             int length = spectrum.Length;
             int coeffCount = cosines.GetLength(0);

src/AudioAnalysisTools/FindMatchingEvents.cs

@@ -596,7 +596,7 @@ public static Tuple<double[]> Execute_MFCC_XCOR(double[,] target, double dynamic
             //set up the matrix of cosine coefficients
             int coeffCount = 12; //only use first 12 coefficients.
             int binCount = target.GetLength(1);  //number of filters in filter bank
-            double[,] cosines = MFCCStuff.Cosines(binCount, coeffCount + 1); //set up the cosine coefficients
+            double[,] cosines = DctMethods.Cosines(binCount, coeffCount + 1); //set up the cosine coefficients
 
             //adjust target's dynamic range to that set by user
             target = SNR.SetDynamicRange(target, 3.0, dynamicRange); //set event's dynamic range

src/AudioAnalysisTools/Harmonics/HarmonicAnalysis.cs

@@ -272,7 +272,7 @@ public static Tuple<double[], double[,]> DetectHarmonicsUsingFormantGap(double[,
             int cols = matrix.GetLength(1);
             double[,] hits = new double[rows, cols];
 
-            double[,] cosines = MFCCStuff.Cosines(dctLength, dctLength); //set up the cosine coefficients
+            double[,] cosines = DctMethods.Cosines(dctLength, dctLength); //set up the cosine coefficients
 
             for (int r = 0; r < rows - dctLength; r++)
             {
@@ -293,7 +293,7 @@ public static Tuple<double[], double[,]> DetectHarmonicsUsingFormantGap(double[,
 
                 //     DataTools.writeBarGraph(array);
 
-                double[] dct = MFCCStuff.DCT(array, cosines);
+                double[] dct = MFCCStuff.CalculateCeptrum(array, cosines);
                 for (int i = 0; i < dctLength; i++)
                 {
                     dct[i] = Math.Abs(dct[i]); //convert to absolute values

src/AudioAnalysisTools/Harmonics/HarmonicParameters.cs

@@ -201,7 +201,7 @@ public static Tuple<double[], double[], int[]> DetectHarmonicsInSpectrogramData(
             var binCount = m.GetLength(1);
 
             //set up the cosine coefficients
-            double[,] cosines = MFCCStuff.Cosines(binCount, binCount);
+            double[,] cosines = DctMethods.Cosines(binCount, binCount);
 
             // set up time-frame arrays to store decibels, formant intensity and max index.
             var dBArray = new double[rowCount];
@@ -265,7 +265,7 @@ public static Tuple<double[], double[], int[]> DetectHarmonicsInSpectrogramData(
                 // set the first four values in the returned DCT coefficients to 0.
                 // We require a minimum of three formants, that is, two harmonic intervals.
                 int lowerDctBound = 4;
-                var dctCoefficients = Oscillations2012.DoDct(normXr, cosines, lowerDctBound);
+                var dctCoefficients = DctMethods.DoDct(normXr, cosines, lowerDctBound);
                 int indexOfMaxValue = DataTools.GetMaxIndex(dctCoefficients);
                 intensity[t] = dctCoefficients[indexOfMaxValue];
                 maxIndexArray[t] = indexOfMaxValue;

src/AudioAnalysisTools/Ocillations/Oscillations2014.cs

@@ -916,7 +916,7 @@ public static double[] GetSpectralIndex_Osc(AudioRecording recordingSegment, int
         public static void GetOscillationUsingDct(double[] array, double framesPerSecond, double[,] cosines, out double oscilFreq, out double period, out double intenisty)
         {
             var modifiedArray = DataTools.SubtractMean(array);
-            var dctCoeff = MFCCStuff.DCT(modifiedArray, cosines);
+            var dctCoeff = MFCCStuff.CalculateCeptrum(modifiedArray, cosines);
 
             // convert to absolute values because not interested in negative values due to phase.
             for (int i = 0; i < dctCoeff.Length; i++)

tests/Acoustics.Test/AudioAnalysisTools/HarmonicAnalysis/HarmonicAlgorithmTests.cs

@@ -136,7 +136,7 @@ public void TestHarmonicsAlgorithmOn1000HertzHarmonic()
         public void TestCosinesMatrixForDct()
         {
             // get an 8 x 8 matrix.
-            double[,] cosineBasisFunctions = MFCCStuff.Cosines(8, 8);
+            double[,] cosineBasisFunctions = DctMethods.Cosines(8, 8);
 
             //following line writes matrix of cos values for checking.
             var outputDir = new FileInfo(Path.Join(this.TestOutputDirectory.FullName, "Cosines.csv"));