removed calculation of R3D

Issue #276 Removed all references to spectral index R3D and to calculation of it.
QutEcoacoustics · Nov 25, 2019 · 96354c9 · 96354c9
1 parent 781d0a3
commit 96354c9
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Showing 4 changed files with 22 additions and 61 deletions.
diff --git a/src/AudioAnalysisTools/Indices/IndexCalculate.cs b/src/AudioAnalysisTools/Indices/IndexCalculate.cs
@@ -438,13 +438,6 @@ public static IndexCalculateResult Analysis(
             spectralIndices.RVT = sptInfo.RvtSpectrum;
             spectralIndices.RPS = sptInfo.RpsSpectrum;
             spectralIndices.RNG = sptInfo.RngSpectrum;
-            spectralIndices.R3D = sptInfo.R3DSpectrum;
-
-            //images for debugging
-            //ImageTools.DrawMatrix(dspOutput3.amplitudeSpectrogram, @"C:\SensorNetworks\Output\BAC\HiResRidge\dspOutput3.amplitudeSpectrogram.png");
-            //ImageTools.DrawMatrix(ridgeSpectrogram,                @"C:\SensorNetworks\Output\BAC\HiResRidge\ridgeSpectrogram.png");
-            //ImageTools.DrawMatrix(sptInfo.RvtSpectrum,             @"C:\SensorNetworks\Output\BAC\HiResRidge\ridgeSpectrum.png");
-
             summaryIndices.SptDensity = sptInfo.TrackDensity;
 
             // these are two other indices that I tried but they do not seem to add anything of interest.

diff --git a/src/AudioAnalysisTools/Indices/SpectralIndexValues.cs b/src/AudioAnalysisTools/Indices/SpectralIndexValues.cs
@@ -163,31 +163,29 @@ public static Image CreateImageOfSpectralIndices(SpectralIndexValues spectralInd
 
         /// <summary>
         /// Gets or sets the oscillation spectral index index. Created October 2018.
+        /// 6.
         /// </summary>
         public double[] OSC { get; set; }
 
-        // 8: Sum of Spectral Ridges in Horizontal, postive and neg slope directions (RHZ+RPS+RNG)
-        public double[] R3D { get; set; }
-
         /// <summary>
         /// Gets or sets PMN = Power Minus Noise.
-        /// PMN is measured in decibels but should replace POW as the average decibel spectrogram.
+        /// 7: PMN is measured in decibels but should replace POW as the average decibel spectrogram.
         /// </summary>
         public double[] PMN { get; set; }
 
-        // 9: Spectral Ridges Horizontal
+        // 8: Spectral Ridges Horizontal
         public double[] RHZ { get; set; }
 
-        // 10: Spectral Ridges Vertical
+        // 9: Spectral Ridges Vertical
         public double[] RVT { get; set; }
 
-        // 11: Spectral Ridges Positive slope
+        // 10: Spectral Ridges Positive slope
         public double[] RPS { get; set; }
 
-        // 12: Spectral Ridges Negative Slope
+        // 11: Spectral Ridges Negative Slope
         public double[] RNG { get; set; }
 
-        // 13: Spectral Peak Tracks
+        // 12: Spectral Peak Tracks
         public double[] SPT { get; set; }
 
         // This property only calculated for ACI when zooming

diff --git a/src/AudioAnalysisTools/SpectralPeakTracks.cs b/src/AudioAnalysisTools/SpectralPeakTracks.cs
@@ -1,4 +1,4 @@
-// <copyright file="SpectralPeakTracks.cs" company="QutEcoacoustics">
+// <copyright file="SpectralPeakTracks.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>
 
@@ -16,7 +16,7 @@ namespace AudioAnalysisTools
     /// </summary>
     public class SpectralPeakTracks
     {
-        private static readonly string[] RidgeKeys = { "SPT", "RVT", "RHZ", "RPS", "RNG", "R3D" };
+        private static readonly string[] RidgeKeys = { "SPT", "RVT", "RHZ", "RPS", "RNG" };
 
         /// <summary>
         /// Initializes a new instance of the <see cref="SpectralPeakTracks"/> class.
@@ -31,7 +31,6 @@ public SpectralPeakTracks(double[,] dBSpectrogram, double peakThreshold)
             // It was changed while in Toulon to the following line which does not require a threshold.
             // this.GetRidgeSpectraVersion1(dBSpectrogram, ridgeThreshold: 4.0);
             this.GetRidgeSpectraVersion2(dBSpectrogram);
-            this.CalculateCombinationOfThreeDirections();
         }
 
         public double[,] Peaks { get; private set; }
@@ -69,11 +68,6 @@ public SpectralPeakTracks(double[,] dBSpectrogram, double peakThreshold)
         /// </summary>
         public double[] RngSpectrum { get; private set; }
 
-        /// <summary>
-        /// gets three directions ridge value
-        /// </summary>
-        public double[] R3DSpectrum { get; private set; }
-
         public static string[] GetDefaultRidgeKeys()
         {
             return RidgeKeys;
@@ -324,23 +318,6 @@ public void GetPeakTracksSpectrum(double[,] dBSpectrogram, double dBThreshold)
             //this.AvTrackDuration = TimeSpan.FromSeconds(avFramesPerTrack / framesPerSecond);
         }
 
-        /// <summary>
-        /// Calculates the max of the Horizontal, positive and negative slope ridges.
-        /// Could alternatively calculate the sum of the Horizontal, positive and negative slope ridges.
-        /// </summary>
-        public void CalculateCombinationOfThreeDirections()
-        {
-            this.R3DSpectrum = new double[this.RhzSpectrum.Length];
-            for (int i = 0; i < this.RhzSpectrum.Length; i++)
-            {
-                var array = new[] { this.RhzSpectrum[i], this.RpsSpectrum[i], this.RngSpectrum[i] };
-                this.R3DSpectrum[i] = array.Max();
-
-                // alternatively, sum the indices
-                //this.R3DSpectrum[i] = this.RhzSpectrum[i] + this.RpsSpectrum[i] + this.RngSpectrum[i];
-            }
-        }
-
         // ################################### STATIC METHODS BELOW HERE ########################################
 
         /// <summary>

diff --git a/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs b/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs
@@ -135,93 +135,86 @@ public void TestOfSpectralIndices()
             var spectralIndices = results.SpectralIndexValues;
 
             // TEST the SPECTRAL INDICES
-            // After serialising the expected vector and writing to the resources directory, comment the Binary.Serialise line.
+            // After serializing the expected vector and writing to the resources directory, comment the Binary.Serialise line.
 
-            // ACI
+            // 1:ACI
             var expectedSpectrumFile = new FileInfo(resourcesDir + "\\ACI.bin");
 
             //Binary.Serialize(expectedSpectrumFile, spectralIndices.ACI);
             var expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.ACI, AllowedDelta);
 
-            // BGN
+            // 2:BGN
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\BGN.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.BGN);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.BGN, AllowedDelta);
 
-            // CVR
+            // 3:CVR
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\CVR.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.CVR);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.CVR, AllowedDelta);
 
-            // ENT
+            // 4:ENT
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\ENT.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.ENT);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.ENT, AllowedDelta);
 
-            // EVN
+            // 5:EVN
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\EVN.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.EVN);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.EVN, AllowedDelta);
 
-            // OSC
+            // 6:OSC
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\OSC.bin");
 
             //Binary.Serialize(expectedSpectrumFile, spectralIndices.OSC);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.OSC, AllowedDelta);
 
-            // PMN
+            // 7:PMN
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\PMN.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.PMN);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.PMN, AllowedDelta);
 
-            // R3D
-            expectedSpectrumFile = new FileInfo(resourcesDir + "\\R3D.bin");
-
-            // Binary.Serialize(expectedSpectrumFile, spectralIndices.R3D);
-            expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
-            CollectionAssert.That.AreEqual(expectedVector, spectralIndices.R3D, AllowedDelta);
-
-            // RHZ
+            // 8:RHZ
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\RHZ.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.RHZ);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.RHZ, AllowedDelta);
 
-            // RNG
+            // 9:RNG
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\RNG.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.RNG);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.RNG, AllowedDelta);
 
-            // RPS
+            // 10:RPS
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\RPS.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.RPS);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.RPS, AllowedDelta);
 
-            // RVT
+            // 11:RVT
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\RVT.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.RVT);
             expectedVector = Binary.Deserialize<double[]>(expectedSpectrumFile);
             CollectionAssert.That.AreEqual(expectedVector, spectralIndices.RVT, AllowedDelta);
 
-            // SPT
+            // 12:SPT
             expectedSpectrumFile = new FileInfo(resourcesDir + "\\SPT.bin");
 
             // Binary.Serialize(expectedSpectrumFile, spectralIndices.SPT);