Created DataProcessing class plus two new test classes

Issue#252 set up two new testing classes but have not yet implemented any tests. Added new data processing class because ContentDescription class was gettgin too large.
QutEcoacoustics · Sep 16, 2019 · e5645d1 · e5645d1
1 parent 7747fd5
commit e5645d1
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Showing 13 changed files with 594 additions and 459 deletions.
diff --git a/src/AudioAnalysisTools/AudioAnalysisTools.csproj b/src/AudioAnalysisTools/AudioAnalysisTools.csproj
@@ -248,6 +248,7 @@
     <Compile Include="ContentDescriptionTools\ContentTypes\SilverEyeMezTasmanIs.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\WindLight1.cs" />
     <Compile Include="ContentDescriptionTools\ContentVisualization.cs" />
+    <Compile Include="ContentDescriptionTools\DataProcessing.cs" />
     <Compile Include="ContentDescriptionTools\DescriptionResult.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\RainHeavy1.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\WindStrong1.cs" />

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentDescription.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentDescription.cs
diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/BaseContentType.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/BaseContentType.cs
@@ -1,12 +1,11 @@
-// <copyright file="WindStrong1.cs" company="QutEcoacoustics">
+// <copyright file="BaseContentType.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.ContentDescriptionTools.ContentTypes
 {
     using System.Collections.Generic;
     using System.IO;
-    using System.Linq;
     using TowseyLibrary;
 
     public abstract class BaseContentType
@@ -38,7 +37,7 @@ public abstract class BaseContentType
         // The all important template that is used to find an acoustic content type.
         // These are calculate, written to a csv file and then appropriate parts are copied into a dictionary declaration such as this.
         // The arrays will all be of same length but will vary from length = 1 to 16 or potentially 256.
-        private static readonly Dictionary<string, double[]> SilverEyeTemplate = new Dictionary<string, double[]>
+        private static readonly Dictionary<string, double[]> Template = new Dictionary<string, double[]>
         {
             ["ACI"] = new[] { 0.086, 0.043, 0.041, 0.023, 0.032, 0.027, 0.029, 0.031, 0.032, 0.032, 0.034, 0.069, 0.033, 0.024, 0.018, 0.018 },
             ["ENT"] = new[] { 0.124, 0.112, 0.146, 0.163, 0.157, 0.157, 0.143, 0.122, 0.113, 0.095, 0.087, 0.121, 0.075, 0.060, 0.054, 0.067 },
@@ -63,11 +62,11 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
         /// </summary>
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var birdIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(birdIndices, ReductionFactor);
-            var freqBinBounds = ContentDescription.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
-            reducedIndices = ContentDescription.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var birdIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(birdIndices, ReductionFactor);
+            var freqBinBounds = DataProcessing.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
+            reducedIndices = DataProcessing.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/BirdMorningChorus1.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/BirdMorningChorus1.cs
@@ -1,4 +1,4 @@
-// <copyright file="BirdMorningChorus1.cs" company="QutEcoacoustics">
+// <copyright file="BirdChorus1.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>
 
@@ -13,11 +13,12 @@ public class BirdMorningChorus1
     {
         //TEMPLATE DESCRIPTION
         // Name of the template
-        public const string Name = "BirdMorningChorus1";
+        public const string Name = "BirdChorus1";
 
         // The TEMPLATE PROVENANCE
         // The source file name from which the indices are extracted.
         private const string BaseName = "SM304256_0+1_20151114_041652";
+        private const string Location = "Mezzanine, Tasman Island";
 
         //THESE ARE SPECIFIC ROW BOUNDS FOR PREPARING THIS TEMPLATE
         // The freq bins will be averaged over the time period.
@@ -44,15 +45,15 @@ public class BirdMorningChorus1
 
         public static KeyValuePair<string, double> GetContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
 
             // remove first two freq bins and last four freq bins
             int bottomBin = 2;
             int topBin = 11;
-            reducedIndices = ContentDescription.ApplyBandPass(reducedIndices, bottomBin, topBin);
+            reducedIndices = DataProcessing.ApplyBandPass(reducedIndices, bottomBin, topBin);
 
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(BirdChorusTemplate);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(BirdChorusTemplate);
 
             //Get Euclidian distance and normalize the distance
             var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
@@ -63,9 +64,9 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
 
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var birdIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(birdIndices, ReductionFactor);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var birdIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(birdIndices, ReductionFactor);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/RainHeavy1.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/RainHeavy1.cs
@@ -13,7 +13,7 @@ public class RainHeavy1
         public const string Name = "HeavyRain1";
         private const int ReductionFactor = 16;
 
-        private static Dictionary<string, double[]> StrongRainTemplate = new Dictionary<string, double[]>
+        private static readonly Dictionary<string, double[]> HeavyRainTemplate = new Dictionary<string, double[]>
         {
             ["ACI"] = new[] { 0.076, 0.046, 0.167, 0.360, 0.426, 0.443, 0.545, 0.595, 0.564, 0.612, 0.659, 0.570, 0.542, 0.520, 0.485, 0.485 },
             ["ENT"] = new[] { 0.065, 0.061, 0.176, 0.289, 0.249, 0.255, 0.296, 0.292, 0.262, 0.386, 0.462, 0.262, 0.222, 0.243, 0.217, 0.205 },
@@ -24,9 +24,9 @@ public class RainHeavy1
 
         public static KeyValuePair<string, double> GetRainContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(StrongRainTemplate);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(HeavyRainTemplate);
 
             //Get Euclidian distance and normalise the distance
             var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
@@ -45,8 +45,8 @@ public static KeyValuePair<string, double> GetRainContent(Dictionary<string, dou
 
         public static Dictionary<string, double[]> GetTemplate(Dictionary<string, double[,]> dictionaryOfIndices)
         {
-            var windIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(windIndices, ReductionFactor);
+            var windIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(windIndices, ReductionFactor);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/RainLight1.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/RainLight1.cs
@@ -38,9 +38,9 @@ public class RainLight1
 
         public static KeyValuePair<string, double> GetContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(LightRainTemplate);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(LightRainTemplate);
 
             //Get Euclidian distance and normalise the distance
             var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
@@ -58,9 +58,9 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
         /// </summary>
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var windIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(windIndices, ReductionFactor);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var windIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(windIndices, ReductionFactor);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/SilverEyeMezTasmanIs.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/SilverEyeMezTasmanIs.cs
@@ -4,7 +4,6 @@
 
 namespace AudioAnalysisTools.ContentDescriptionTools.ContentTypes
 {
-    using System;
     using System.Collections.Generic;
     using System.IO;
     using System.Linq;
@@ -50,20 +49,19 @@ public class SilverEyeMezTasmanIs
 
         public static KeyValuePair<string, double> GetContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
 
-            //var freqBinBounds = ContentDescription.GetFreqBinBounds(BottomFreq, TopFreq);
-            //reducedIndices = ContentDescription.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
-
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(SilverEyeTemplate);
+            //var freqBinBounds = DataProcessing.GetFreqBinBounds(BottomFreq, TopFreq);
+            //reducedIndices = DataProcessing.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
+            //var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            //var templateVector = DataProcessing.ConvertDictionaryToVector(SilverEyeTemplate);
 
             //Get Euclidian distance and normalize the distance
             // Now pass the template up the full frequency spectrum to get a spectrum of scores.
-            var spectralScores = ContentDescription.ScanSpectrumWithTemplate(SilverEyeTemplate, reducedIndices);
+            var spectralScores = DataProcessing.ScanSpectrumWithTemplate(SilverEyeTemplate, reducedIndices);
 
             // Now check how much of spectral weight is in the correct freq band ie between 3-4 kHz.
-            var freqBinBounds = ContentDescription.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
+            var freqBinBounds = DataProcessing.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
             double callSum = DataTools.Subarray(spectralScores, freqBinBounds[0], freqBinBounds[1]).Sum();
             double totalSum = DataTools.Subarray(spectralScores, 1, spectralScores.Length - 3).Sum();
             double score = callSum / totalSum;
@@ -73,11 +71,11 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
 
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var birdIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(birdIndices, ReductionFactor);
-            var freqBinBounds = ContentDescription.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
-            reducedIndices = ContentDescription.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var birdIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(birdIndices, ReductionFactor);
+            var freqBinBounds = DataProcessing.GetFreqBinBounds(BottomFreq, TopFreq, FreqBinCount);
+            reducedIndices = DataProcessing.ApplyBandPass(reducedIndices, freqBinBounds[0], freqBinBounds[1]);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/WindLight1.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/WindLight1.cs
@@ -38,12 +38,12 @@ public class WindLight1
 
         public static KeyValuePair<string, double> GetContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
             reducedIndices.Remove("ENT");
             LightWindTemplate.Remove("ENT");
 
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(LightWindTemplate);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(LightWindTemplate);
 
             var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
 
@@ -54,9 +54,9 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
 
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var windIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(windIndices, ReductionFactor);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var windIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(windIndices, ReductionFactor);
             return reducedIndices;
         }
 

diff --git a/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/WindStrong1.cs b/src/AudioAnalysisTools/ContentDescriptionTools/ContentTypes/WindStrong1.cs
@@ -38,9 +38,9 @@ public class WindStrong1
 
         public static KeyValuePair<string, double> GetContent(Dictionary<string, double[]> oneMinuteOfIndices)
         {
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
-            var oneMinuteVector = ContentDescription.ConvertDictionaryToVector(reducedIndices);
-            var templateVector = ContentDescription.ConvertDictionaryToVector(StrongWindTemplate);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, ReductionFactor);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(StrongWindTemplate);
 
             var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
 
@@ -51,9 +51,9 @@ public static KeyValuePair<string, double> GetContent(Dictionary<string, double[
 
         public static Dictionary<string, double[]> GetTemplate(DirectoryInfo dir)
         {
-            var dictionaryOfIndices = ContentDescription.ReadIndexMatrices(dir, BaseName);
-            var windIndices = ContentDescription.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
-            var reducedIndices = ContentDescription.ReduceIndicesByFactor(windIndices, ReductionFactor);
+            var dictionaryOfIndices = DataProcessing.ReadIndexMatrices(dir, BaseName);
+            var windIndices = DataProcessing.AverageIndicesOverMinutes(dictionaryOfIndices, StartRowId, EndRowId);
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(windIndices, ReductionFactor);
             return reducedIndices;
         }