Removed references to R3D identified by Anthony

Issue #276 Removed references to R3D identified by Anthony
Also fixed two failed unit tests.

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/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/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

@@ -366,7 +366,7 @@ public void GetPeakTracksSpectrum(double[,] dBSpectrogram, double dBThreshold)
         } // 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

@@ -98,7 +98,7 @@ 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);
@@ -207,7 +207,7 @@ 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);

tests/Acoustics.Test/AudioAnalysisTools/LongDurationSpectrograms/Zooming/ZoomCommonTests.cs

@@ -63,8 +63,8 @@ public void TestImagesHaveCorrectLength(double renderScale, int expectedWidth)
             var config = new LdSpectrogramConfig()
             {
                 // same color map to reduce memory stress for test
-                ColorMap1 = SpectrogramConstants.RGBMap_BGN_PMN_R3D,
-                ColorMap2 = SpectrogramConstants.RGBMap_BGN_PMN_R3D,
+                ColorMap1 = SpectrogramConstants.RGBMap_BGN_PMN_EVN,
+                ColorMap2 = SpectrogramConstants.RGBMap_BGN_PMN_EVN,
             };
 
             var generationData = new IndexGenerationData()