Issue #252 Set up new data structures for content description

Issue #252 Set up new data structures for content description based on discussion with Anthony. Separate out main template information into yaml files.

src/AnalysisConfigFiles/ContentDescriptionTemplateManifest.yml

@@ -0,0 +1,111 @@
+--- 
+# WARNING!!! The keys (i.e. root name of each object below) MUST BE EXACTLY the SAME as those 
+#            declared in the class InitialiseIndexProperties (starting at line 30).
+# The root object name maps to the Key property on the IndexProperties class
+# and to the members in the class SummaryIndexValues:SummaryIndexBase
+
+RainLight1:
+  TemplateId: 0
+  Name: "Light Rain 1"
+  Comment: "Detects light rain."
+  SourceFileName: "SM304256_0+1_20151114_071652"
+  # Status can be "locked", etc
+  Status: "locked"
+  RecordingLocation: "Mezzanine, Tasman Is, Tasmania"
+  RecordingDateTime: "2015-11-14 07:16:52 +1100"
+  FeatureExtractionAlgorithm: 1
+  # Temporal Selection - minutes are inclusive"
+  StartMinute: 32
+  EndMinute: 36
+  TemporalReduction: "Average"
+  #Spectral Processing
+  SpectralReductionFactor: 16
+  # Frequency band selection
+  BandMinHz:
+  BandMaxHz:
+WindStrong1:
+  TemplateId: 01
+  Name: Strong Wind 1
+  Comment: "Detects strong wind."
+  SourceFileName: "SM304256_0+1_20151114_011652"
+  # Status can be "locked", etc
+  Status: "locked"
+  RecordingLocation: "Mezzanine, Tasman Is, Tasmania"
+  RecordingDateTime: "2015-11-14 01:16:52 +1100"
+  FeatureExtractionAlgorithm: 1
+  # Temporal Selection - minutes are inclusive"
+  StartMinute: 2
+  EndMinute: 27
+  TemporalReduction: "Average"
+  #Spectral Processing
+  SpectralReductionFactor: 16
+  # Frequency band selection
+  BandMinHz:
+  BandMaxHz:
+WindLight1:
+  TemplateId: 02
+  Name: Light Wind 1
+  Comment: "Detects light wind."
+  SourceFileName: "SM304256_0+1_20151114_021652"
+  # Status can be "locked", etc
+  Status: "locked"
+  RecordingLocation: "Mezzanine, Tasman Is, Tasmania"
+  RecordingDateTime: "2015-11-14 02:16:52 +1100"
+  # NOTE: Remove the ENT index before applying this template
+  FeatureExtractionAlgorithm: 1
+  # Temporal Selection - minutes are inclusive"
+  StartMinute: 50
+  EndMinute: 53
+  TemporalReduction: "Average"
+  #Spectral Processing
+  SpectralReductionFactor: 16
+  # Frequency band selection
+  BandMinHz:
+  BandMaxHz:
+BirdChorus1:
+  TemplateId: 03
+  Name: Bird Chorus
+  Comment: "Detects chorus of bird song."
+  SourceFileName: "SM304256_0+1_20151114_041652"
+  # Status can be "locked", etc
+  Status: "locked"
+  RecordingLocation: "Mezzanine, Tasman Is, Tasmania"
+  RecordingDateTime: "2015-11-14 04:16:52 +1100"
+  # Only want the interval 2-8 kHz for bird morning chorus.
+  # After reducing 256 freq bins to 16, each bin has width 689Hz.
+  # Therefore to get band 2-8 kHz, need to remove the bottom two freq bins and the top four freq bins.
+  # This leaves a template with 10 freq bins.
+  FeatureExtractionAlgorithm: 1
+  # Temporal Selection - minutes are inclusive"
+  StartMinute: 22
+  EndMinute: 23
+  TemporalReduction: "Average"
+  #Spectral Processing
+  SpectralReductionFactor: 16
+  # Frequency band selection - select freq bins 2 to 11
+  BandMinHz: 2000
+  BandMaxHz: 8000
+SilverEye:
+  TemplateId: 04
+  Name: Silver Eye
+  Comment: "Detects Silver Eye song in a Tasman Island recording."
+  SourceFileName: "SM304256_0+1_20151114_071652"
+  # Status can be "locked", etc
+  Status: "locked"
+  RecordingLocation: "Mezzanine, Tasman Is, Tasmania"
+  RecordingDateTime: "2015-11-14 07:16:52 +1100"
+  # Only want the interval 3-4 kHz for Silver-eye band.
+  # After reducing 256 freq bins to 16 bins, each bin has width 689Hz.
+  # Therefore to get band 3-4 kHz, this leaves a template with 2 or 3 freq bins which are then averaged.
+  # So each index ends up with only one value.
+  FeatureExtractionAlgorithm: 1
+  # Temporal Selection - minutes are inclusive"
+  StartMinute: 6
+  EndMinute: 11
+  TemporalReduction: "Average"
+  #Spectral Processing
+  SpectralReductionFactor: 16
+  # Frequency band selection
+  BandMinHz: 3000
+  BandMaxHz: 4000
+

src/AnalysisConfigFiles/ContentDescriptionTemplates.yml

@@ -0,0 +1,86 @@
+--- 
+RainLight1:
+  TemplateId: 0
+  Name: "Light Rain 1"
+  Status: "locked"
+  Template:
+    ACI: [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: [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]
+    EVN: [0.136, 0.009, 0.022, 0.051, 0.072, 0.092, 0.109, 0.150, 0.175, 0.176, 0.193, 0.155, 0.171, 0.135, 0.109, 0.133]
+    BGN: [0.366, 0.249, 0.181, 0.148, 0.122, 0.111, 0.106, 0.105, 0.104, 0.111, 0.111, 0.111, 0.105, 0.100, 0.090, 0.048]
+    PMN: [0.182, 0.076, 0.243, 0.459, 0.470, 0.501, 0.592, 0.651, 0.625, 0.699, 0.792, 0.599, 0.572, 0.550, 0.490, 0.488]
+  FeatureExtractionAlgorithm: 1
+  StartMinute: 32
+  EndMinute: 36
+  TemporalReduction: "Average"
+  SpectralReductionFactor: 16
+  BandMinHz:
+  BandMaxHz:
+WindStrong1:
+  TemplateId: 01
+  Name: Strong Wind 1
+  Status: "locked"
+  Template:
+    ACI: [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: [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]
+    EVN: [0.376, 0.440, 0.590, 0.621, 0.648, 0.621, 0.565, 0.363, 0.273, 0.191, 0.164, 0.221, 0.104, 0.040, 0.017, 0.032]
+    BGN: [0.472, 0.360, 0.273, 0.199, 0.156, 0.121, 0.096, 0.085, 0.075, 0.069, 0.064, 0.061, 0.060, 0.058, 0.054, 0.026]
+    PMN: [0.468, 0.507, 0.687, 0.743, 0.757, 0.751, 0.665, 0.478, 0.391, 0.317, 0.276, 0.367, 0.187, 0.109, 0.071, 0.096]
+  FeatureExtractionAlgorithm: 1
+  StartMinute: 2
+  EndMinute: 27
+  TemporalReduction: "Average"
+  SpectralReductionFactor: 16
+  BandMinHz:
+  BandMaxHz:
+WindLight1:
+  TemplateId: 02
+  Name: Light Wind 1
+  Status: "locked"
+  Template:
+    ACI: [0.072, 0.035, 0.015, 0.008, 0.008, 0.009, 0.016, 0.018, 0.017, 0.015, 0.020, 0.022, 0.029, 0.026, 0.027, 0.098]
+    ENT: [0.063, 0.069, 0.071, 0.059, 0.052, 0.051, 0.050, 0.050, 0.050, 0.050, 0.050, 0.052, 0.051, 0.050, 0.051, 0.058]
+    EVN: [0.160, 0.099, 0.077, 0.023, 0.009, 0.009, 0.005, 0.004, 0.003, 0.004, 0.003, 0.006, 0.002, 0.004, 0.003, 0.015]
+    BGN: [0.387, 0.257, 0.151, 0.094, 0.069, 0.055, 0.049, 0.045, 0.042, 0.041, 0.041, 0.042, 0.043, 0.044, 0.043, 0.017]
+    PMN: [0.228, 0.199, 0.179, 0.087, 0.065, 0.048, 0.042, 0.034, 0.035, 0.035, 0.036, 0.038, 0.038, 0.037, 0.044, 0.081]
+  FeatureExtractionAlgorithm: 1
+  StartMinute: 50
+  EndMinute: 53
+  TemporalReduction: "Average"
+  SpectralReductionFactor: 16
+  BandMinHz:
+  BandMaxHz:
+BirdChorus1:
+  TemplateId: 03
+  Name: Bird Chorus
+  Status: "locked"
+  Template:
+    ACI: [0.274, 0.366, 0.591, 0.820, 0.997, 0.975, 0.796, 0.846, 0.605, 0.260]
+    ENT: [0.293, 0.415, 0.804, 0.972, 0.910, 0.876, 0.923, 0.971, 0.840, 0.491]
+    EVN: [0.445, 0.691, 0.291, 0.266, 0.407, 0.417, 0.306, 0.321, 0.199, 0.091]
+    BGN: [0.140, 0.099, 0.072, 0.059, 0.055, 0.051, 0.048, 0.048, 0.045, 0.042]
+    PMN: [0.671, 0.967, 0.924, 0.998, 1.000, 1.000, 0.998, 1.000, 0.952, 0.633]
+  FeatureExtractionAlgorithm: 10
+  StartMinute: 22
+  EndMinute: 23
+  TemporalReduction: "Average"
+  SpectralReductionFactor: 16
+  BandMinHz: 2000
+  BandMaxHz: 8000
+SilverEye:
+  TemplateId: 04
+  Name: Silver Eye
+  Status: "locked"
+  Template:
+    ACI: [0.779]
+    ENT: [0.393]
+    EVN: [0.686]
+    BGN: [0.085]
+    PMN: [0.883]
+  FeatureExtractionAlgorithm: 10
+  StartMinute: 6
+  EndMinute: 11
+  TemporalReduction: "Average"
+  SpectralReductionFactor: 16
+  BandMinHz: 3000
+  BandMaxHz: 4000

src/AnalysisPrograms/Sandpit.cs

@@ -64,8 +64,8 @@ public override Task<int> Execute(CommandLineApplication app)
                 Log.WriteLine("# Start Time = " + tStart.ToString(CultureInfo.InvariantCulture));
 
                 // CONTENT DESCRIPTION
-                //ReadSpectralIndicesFromTwoFalseColourSpectrogramRibbons();
-                ContentDescriptionDev();
+                //ContentDescriptionCreateTemplates();
+                ContentDescriptionApplyTemplates();
 
                 //AnalyseFrogDataSet();
                 //Audio2CsvOverOneFile();
@@ -119,7 +119,35 @@ public override Task<int> Execute(CommandLineApplication app)
             }
         }
 
-        public static void ContentDescriptionDev()
+        public static void ContentDescriptionCreateTemplates()
+        {
+            //PREPARE STRONG WIND TEMPLATE
+            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez02\Towsey.Acoustic");
+            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
+            //WindStrong1.WriteTemplateToFile(ipDir, opDir);
+
+            //PREPARE LIGHT WIND TEMPLATE
+            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez03\Towsey.Acoustic");
+            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
+            //WindLight1.WriteTemplateToFile(ipDir, opDir);
+
+            //PREPARE LIGHT RAIN TEMPLATE
+            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez08\Towsey.Acoustic");
+            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
+            //WindLight1.WriteTemplateToFile(ipDir, opDir);
+
+            //PREPARE BIRD MORNING CHORUS1 TEMPLATE
+            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez05\Towsey.Acoustic");
+            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
+            //BirdMorningChorus1.WriteTemplateToFile(ipDir, opDir);
+
+            //PREPARE MEZZANINE-TASMAN ISLAND SILVER-EYE TEMPLATE
+            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez08\Towsey.Acoustic");
+            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
+            //SilverEyeMezTasmanIs.WriteTemplateToFile(ipDir, opDir);
+        }
+
+        public static void ContentDescriptionApplyTemplates()
         {
             DirectoryInfo[] directories =
             {
@@ -149,7 +177,9 @@ public static void ContentDescriptionDev()
                 new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez24\Towsey.Acoustic"),
             };
 
-            string[] baseNames = { "SM304256_0+1_20151114_001652",
+            string[] baseNames =
+            {
+                "SM304256_0+1_20151114_001652",
                 "SM304256_0+1_20151114_011652",
                 "SM304256_0+1_20151114_021652",
                 "SM304256_0+1_20151114_031652",
@@ -173,42 +203,19 @@ public static void ContentDescriptionDev()
                 "SM304256_0+1_20151114_211652",
                 "SM304256_0+1_20151114_221652",
                 "SM304256_0+1_20151114_231652",
-};
-
-            //PREPARE STRONG WIND TEMPLATE
-            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez02\Towsey.Acoustic");
-            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
-            //WindStrong1.WriteTemplateToFile(ipDir, opDir);
-
-            //PREPARE LIGHT WIND TEMPLATE
-            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez03\Towsey.Acoustic");
-            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
-            //WindLight1.WriteTemplateToFile(ipDir, opDir);
-
-            //PREPARE LIGHT RAIN TEMPLATE
-            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez08\Towsey.Acoustic");
-            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
-            //WindLight1.WriteTemplateToFile(ipDir, opDir);
-
-            //PREPARE BIRD MORNING CHORUS1 TEMPLATE
-            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez05\Towsey.Acoustic");
-            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
-            //BirdMorningChorus1.WriteTemplateToFile(ipDir, opDir);
+            };
 
-            //PREPARE MEZZANINE-TASMAN ISLAND SILVER-EYE TEMPLATE
-            //var ipDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\Mez08\Towsey.Acoustic");
-            //var opDir = new DirectoryInfo(@"C:\Ecoacoustics\Output\ContentDescription");
-            //SilverEyeMezTasmanIs.WriteTemplateToFile(ipDir, opDir);
+            var templatesConfig = new FileInfo(@"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\ContentDescriptionTemplates.yml");
 
-            var contentPlots = ContentDescription.ContentDescriptionOfMultipleRecordingFiles(directories, baseNames);
+            var contentPlots = ContentDescription.ContentDescriptionOfMultipleRecordingFiles(directories, baseNames, templatesConfig);
 
             // Attach content description plots to LDFC spectrogram
             var path = Path.Combine(@"C:\Ecoacoustics\Output\Test\Test24HourRecording", "Testing__2Maps.png");
             var ldfcSpectrogram = Image.FromFile(path);
 
             //Write image + contentPlots to file.
             var image = ContentVisualization.DrawLdfcSpectrogramWithContentScoreTracks(ldfcSpectrogram, contentPlots);
-            var path1 = Path.Combine(@"C:\Ecoacoustics\Output\ContentDescription", "Testing_2Maps.CONTENT10.png");
+            var path1 = Path.Combine(@"C:\Ecoacoustics\Output\ContentDescription", "Testing_2Maps.CONTENTnew01.png");
             image.Save(path1);
         }
 

src/AudioAnalysisTools/AudioAnalysisTools.csproj

@@ -241,6 +241,7 @@
     <Compile Include="ActivityAndCover.cs" />
     <Compile Include="BirdClefExperiment1.cs" />
     <Compile Include="ChannelIntegrity.cs" />
+    <Compile Include="ContentDescriptionTools\ContentAlgorithms.cs" />
     <Compile Include="ContentDescriptionTools\ContentDescription.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\BaseContentType.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\RainLight1.cs" />
@@ -252,6 +253,8 @@
     <Compile Include="ContentDescriptionTools\DescriptionResult.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\RainHeavy1.cs" />
     <Compile Include="ContentDescriptionTools\ContentTypes\WindStrong1.cs" />
+    <Compile Include="ContentDescriptionTools\ContentTemplate.cs" />
+    <Compile Include="ContentDescriptionTools\TemplateCollection.cs" />
     <Compile Include="CrossCorrelation.cs" />
     <Compile Include="DSP\Clipping.cs" />
     <Compile Include="DSP\DSP_Filters.cs" />

src/AudioAnalysisTools/ContentDescriptionTools/ContentAlgorithms.cs

@@ -0,0 +1,31 @@
+// <copyright file="ContentAlgorithms.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>
+
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace AudioAnalysisTools.ContentDescriptionTools
+{
+    using TowseyLibrary;
+
+    public static class ContentAlgorithms
+    {
+        public static double GetContent1(Dictionary<string, double[]> oneMinuteOfIndices, ContentTemplate template, Dictionary<string, double[]> templateIndices)
+        {
+            var reductionFactor = template.SpectralReductionFactor;
+            var reducedIndices = DataProcessing.ReduceIndicesByFactor(oneMinuteOfIndices, reductionFactor);
+            var oneMinuteVector = DataProcessing.ConvertDictionaryToVector(reducedIndices);
+            var templateVector = DataProcessing.ConvertDictionaryToVector(templateIndices);
+
+            var distance = DataTools.EuclideanDistance(templateVector, oneMinuteVector);
+
+            //normalise the distance
+            distance /= Math.Sqrt(templateVector.Length);
+            return 1 - distance;
+        }
+    }
+}