Merge pull request #277 from QutEcoacoustics/Remove-Spectral-Index-R3…

…D-Issue-#276

Removed calculation of R3D, Closes #246

src/AnalysisConfigFiles/IndexPropertiesConfig.HiRes.yml

@@ -522,17 +522,6 @@ RNG:
   CalculateNormBounds: true
   ProjectID: Acoustic Indices
   Units: "tracks/s"
-R3D:
-  Name: spectralR3D
-  Comment: "Spectrum of max value of horizontal, positive and negative slope ridges per sec."
-  DataType: double[]
-  DefaultValue: 0.0
-  DoDisplay: true
-  NormMin: 0.15
-  NormMax: 1.0
-  CalculateNormBounds: true
-  ProjectID: Acoustic Indices
-  Units: "tracks/s"
 SPT:
   Name: spectralSPT
   Comment: "Spectrum of average number of spectral Peak Tracks per second within each freq bin."

src/AnalysisConfigFiles/IndexPropertiesConfig.Zooming.yml

@@ -616,17 +616,6 @@ RNG:
   CalculateNormBounds: false
   ProjectID: Acoustic Indices
   Units: "tracks/s"
-R3D:
-  Name: spectralR3D
-  Comment: "Spectrum of max value of horizontal, positive and negative slope ridges per sec."
-  DataType: double[]
-  DefaultValue: 0.0
-  DoDisplay: true
-  NormMin: 0.15
-  NormMax: 1.0
-  CalculateNormBounds: false
-  ProjectID: Acoustic Indices
-  Units: "tracks/s"
 SPT:
   Name: spectralSPT
   Comment: "Spectrum of average number of spectral Peak Tracks per second within each freq bin."

src/AnalysisConfigFiles/IndexPropertiesConfig.yml

@@ -664,20 +664,6 @@ RNG:
   #CalculateNormMax: false
   ProjectID: Acoustic Indices
   Units: "tracks/s"
-R3D:
-  Name: spectralR3D
-  Comment: "Spectrum of max value of horizontal, positive and negative slope ridges per sec."
-  DataType: double[]
-  DefaultValue: 0.0
-  DoDisplay: true
-  NormMin: 0.15
-  NormMax: 1.0
-  CalculateNormBounds: true
-  # Merge conflict values from https://github.com/QutEcoacoustics/audio-analysis/pull/233
-  #CalculateNormMin: false
-  #CalculateNormMax: false
-  ProjectID: Acoustic Indices
-  Units: "tracks/s"
 SPT:
   Name: spectralSPT
   Comment: "Spectrum of average number of spectral Peak Tracks per second within each freq bin."

src/AnalysisConfigFiles/SpectrogramFalseColourConfig.yml

@@ -4,7 +4,7 @@
 # It should NOT contain dynamic data (like file names or analysis types)
 
 ColorMap1: "ACI-ENT-EVN"
-ColorMap2: "BGN-PMN-R3D"
+ColorMap2: "BGN-PMN-EVN"
 
 # The ColourFilter parameter determines how much the low index values are emphasized or de-emphasized.
 # The purpose is to make low intensity features stand out (emphasis) or become even less obvious (de-emphasis).

src/AnalysisPrograms/Recognizers/Base/RecognizerBase.cs

@@ -196,7 +196,7 @@ private void DrawLongDurationSpectrogram(
                 FalseColourSpectrogramConfig = spectrogramConfig.FullName,
                 IndexPropertiesConfig = ipConfig.FullName,
                 ColourMap1 = "BGN-DMN-EVN",
-                ColourMap2 = "R3D-RVT-SPT", //R3D replaces PHN as new derived index
+                ColourMap2 = "RHZ-RVT-SPT", //R3D replaces PHN as new derived index
                 TemporalScale = hiResTimeScale,
             };
 

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.

src/AudioAnalysisTools/Indices/InitialiseIndexProperties.cs

@@ -73,13 +73,11 @@ public static class InitialiseIndexProperties
 
         //public const string KeYspectralAci = "ACI";
         //public const string KeySpectralBgn = "BGN";
-        //public const string KeYspectralCls = "CLS";
         //public const string KeYspectralCvr = "CVR";
         //public const string KeYspectralEnt = "ENT";
         //public const string KeYspectralEvn = "EVN";
         //public const string KeySpectralOsc = "OSC";
         //public const string KeySpectralPmn = "PMN";
-        //public const string KeySpectralR3D = "R3D";
         //public const string KeySpectralRhz = "RHZ";
         //public const string KeySpectralRng = "RNG";
         //public const string KeySpectralRps = "RPS";

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

src/AudioAnalysisTools/LongDurationSpectrograms/LDSpectrogramConfig.cs

@@ -111,7 +111,7 @@ public static LdSpectrogramConfig ReadYamlToConfig(FileInfo path)
 
         /// <summary>
         /// NOTE: As of August 2015, we are using EVN (event count) in both spectrograms because CVR (cover) is too highly correlated with POW.
-        /// NOTE: As of May 2017, PMN replaces POW and we are using R3D in spectrogram2 because it is less correlated with PMN.
+        /// NOTE: As of May 2017, PMN replaces POW.
         /// </summary>
         public static LdSpectrogramConfig GetDefaultConfig()
         {

src/AudioAnalysisTools/LongDurationSpectrograms/LDSpectrogramRGB.cs

@@ -78,10 +78,10 @@ public class LDSpectrogramRGB
         public static string[] GetArrayOfAvailableKeys()
         {
             // Before May 2017, only the required six spectral indices were incorporated in a dictionary of spectral matrices.
-            // Since May 2017, all the likely available matrices are incorporated into a dictionary. Note the new names for PMN and R3D, previously POW and HPN respectively.
+            // Since May 2017, all the likely available matrices are incorporated into a dictionary. Note the new name for PMN, previously POW.
             // Note 1: This default array will be subsequently over-written by the indices in the IndexPropertiesConfig file if one is available.
-            // Note 1: RHZ, SPT and CVR are correlated with POW and do not add much. CLS is not particularly useful. Currently using R3D
-            // Decmeber 2018: Now all spectral indices are always used in drawing images
+            // Note 1: RHZ, SPT and CVR are correlated with PMN and do not add much.
+            // December 2018: Now all spectral indices are always used in drawing images
             return SpectralIndexValues.Keys;
         }
 

src/AudioAnalysisTools/LongDurationSpectrograms/SpectrogramConstants.cs

@@ -20,16 +20,13 @@ public static class SpectrogramConstants
 
         public const string RGBMap_ACI_ENT_PMN = "ACI-ENT-PMN"; //R-G-B
         public const string RGBMap_ACI_ENT_CVR = "ACI-ENT-CVR"; //R-G-B
-        public const string RGBMap_ACI_ENT_CLS = "ACI-ENT-CLS"; //R-G-B
         public const string RGBMap_ACI_ENT_EVN = "ACI-ENT-EVN"; //R-G-B
         public const string RGBMap_ACI_ENT_SPT = "ACI-ENT-SPT"; //R-G-B
 
         // A second set of RGB mappings based on BGN and PMN.
         public const string RGBMap_BGN_PMN_EVN = "BGN-PMN-EVN"; //R-G-B
         public const string RGBMap_BGN_PMN_SPT = "BGN-PMN-SPT"; //R-G-B
-        public const string RGBMap_BGN_PMN_CLS = "BGN-PMN-CLS"; //R-G-B
         public const string RGBMap_BGN_PMN_OSC = "BGN-PMN-OSC";
-        public const string RGBMap_BGN_PMN_R3D = "BGN-PMN-R3D";
         public const string RGBMap_BGN_PMN_RHZ = "BGN-PMN-RHZ";
         public const string RGBMap_BGN_PMN_CVR = "BGN-PMN-CVR"; //R-G-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>
@@ -389,7 +366,7 @@ public void CalculateCombinationOfThreeDirections()
         } // LocalPeaks()
 
         /// <summary>
-        /// CALCULATEs SPECTRAL PEAK TRACKS: spectralIndices.SPT, RHZ, RVT, RPS, RNG, R3D,
+        /// CALCULATEs SPECTRAL PEAK TRACKS: spectralIndices.SPT, RHZ, RVT, RPS, RNG
         /// This method is only called from IndexCalulate.analysis() when the IndexCalculation Duration is less than 10 seconds,
         /// because need to recalculate background noise etc.
         /// Otherwise the constructor of this class is called: sptInfo = new SpectralPeakTracks(decibelSpectrogram, peakThreshold);

tests/Acoustics.Test/AnalysisPrograms/AnalyzeLongRecordings/TestAnalyzeLongRecording.cs

@@ -98,16 +98,16 @@ public void TestAnalyzeSr22050Recording()
             var resultsDirectory = this.outputDirectory.Combine("Towsey.Acoustic");
             var listOfFiles = resultsDirectory.EnumerateFiles().ToArray();
 
-            Assert.AreEqual(40, listOfFiles.Length);
+            Assert.AreEqual(38, listOfFiles.Length);
 
             var csvCount = listOfFiles.Count(f => f.Name.EndsWith(".csv"));
-            Assert.AreEqual(16, csvCount);
+            Assert.AreEqual(15, csvCount);
 
             var jsonCount = listOfFiles.Count(f => f.Name.EndsWith(".json"));
             Assert.AreEqual(2, jsonCount);
 
             var pngCount = listOfFiles.Count(f => f.Name.EndsWith(".png"));
-            Assert.AreEqual(22, pngCount);
+            Assert.AreEqual(21, pngCount);
 
             var twoMapsImagePath = resultsDirectory.CombineFile("TemporaryRecording1__2Maps.png");
             var twoMapsImage = ImageTools.ReadImage2Bitmap(twoMapsImagePath.FullName);
@@ -207,10 +207,10 @@ public void TestAnalyzeSr64000Recording()
             var resultsDirectory = this.outputDirectory.Combine("Towsey.Acoustic");
             var listOfFiles = resultsDirectory.EnumerateFiles().ToArray();
 
-            Assert.AreEqual(20, listOfFiles.Length);
+            Assert.AreEqual(19, listOfFiles.Length);
 
             var csvCount = listOfFiles.Count(f => f.Name.EndsWith(".csv"));
-            Assert.AreEqual(16, csvCount);
+            Assert.AreEqual(15, csvCount);
 
             var jsonCount = listOfFiles.Count(f => f.Name.EndsWith(".json"));
             Assert.AreEqual(2, jsonCount);
@@ -269,7 +269,7 @@ public void TestAnalyzeSr64000Recording()
             // test number of images - should now be 23
             listOfFiles = resultsDirectory.EnumerateFiles().ToArray();
             pngCount = listOfFiles.Count(f => f.Name.EndsWith(".png"));
-            Assert.AreEqual(23, pngCount);
+            Assert.AreEqual(22, pngCount);
 
             var twoMapsImagePath = resultsDirectory.CombineFile(recordingName + "__2Maps.png");
             var twoMapsImage = ImageTools.ReadImage2Bitmap(twoMapsImagePath.FullName);

tests/Acoustics.Test/AnalysisPrograms/Draw/Zooming/DrawZoomingTests.cs

@@ -53,9 +53,9 @@ public static void ClassInitialize(TestContext context)
 
             // do some basic checks that the indices were generated
             var listOfFiles = ResultsDirectory.EnumerateFiles().ToArray();
-            Assert.AreEqual(20, listOfFiles.Length);
+            Assert.AreEqual(19, listOfFiles.Length);
             var csvCount = listOfFiles.Count(f => f.Name.EndsWith(".csv"));
-            Assert.AreEqual(16, csvCount);
+            Assert.AreEqual(15, csvCount);
             var jsonCount = listOfFiles.Count(f => f.Name.EndsWith(".json"));
             Assert.AreEqual(2, jsonCount);
             var pngCount = listOfFiles.Count(f => f.Name.EndsWith(".png"));