Flying fox recognizer

src/AED/AED.fsproj

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="15.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <Import Project="..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props" Condition="Exists('..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props')" />
+  <Import Project="..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props" Condition="Exists('..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props')" />
   <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
@@ -121,7 +121,7 @@
       <ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them.  For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
     </PropertyGroup>
     <Error Condition="!Exists('..\..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets'))" />
-    <Error Condition="!Exists('..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props'))" />
+    <Error Condition="!Exists('..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props'))" />
   </Target>
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

src/AED/packages.config

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="FSharp.Compiler.Tools" version="10.2.1" targetFramework="net462" />
+  <package id="FSharp.Compiler.Tools" version="10.2.3" targetFramework="net462" />
   <package id="FSharp.Core" version="4.3.4" targetFramework="net462" />
   <package id="FSPowerPack.Community" version="3.0.0.0" targetFramework="net462" />
   <package id="FSPowerPack.Core.Community" version="3.0.0.0" targetFramework="net462" />

src/Acoustics.Shared.FSharp/Acoustics.Shared.FSharp.fsproj

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="15.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <Import Project="..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props" Condition="Exists('..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props')" />
+  <Import Project="..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props" Condition="Exists('..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props')" />
   <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
@@ -154,7 +154,7 @@
       <ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them.  For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
     </PropertyGroup>
     <Error Condition="!Exists('..\..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets'))" />
-    <Error Condition="!Exists('..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\FSharp.Compiler.Tools.10.2.1\build\FSharp.Compiler.Tools.props'))" />
+    <Error Condition="!Exists('..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\FSharp.Compiler.Tools.10.2.3\build\FSharp.Compiler.Tools.props'))" />
   </Target>
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

src/Acoustics.Shared.FSharp/packages.config

@@ -5,7 +5,7 @@
   <package id="Accord.Statistics" version="2.12.0.0" targetFramework="net462" />
   <package id="AForge" version="2.2.5" targetFramework="net462" />
   <package id="AForge.Math" version="2.2.5" targetFramework="net462" />
-  <package id="FSharp.Compiler.Tools" version="10.2.1" targetFramework="net462" />
+  <package id="FSharp.Compiler.Tools" version="10.2.3" targetFramework="net462" />
   <package id="FSharp.Core" version="4.3.4" targetFramework="net462" />
   <package id="FSPowerPack.Community" version="3.0.0.0" targetFramework="net462" />
   <package id="FSPowerPack.Core.Community" version="3.0.0.0" targetFramework="net462" />

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.PteropusSpecies.yml

@@ -0,0 +1,78 @@
+---
+SpeciesName: Pteropus sp.
+CommonName: Flying Fox
+AbbreviatedSpeciesName: PteropusSp
+
+#Proposed Approach:
+#1. Assume that a long recording has been broken into one-minute segments.
+#2. Convert each one-minute segment to a spectrogram.
+#3. Obtain a noise profile for each segment. This is to be used later to remove insect chorusing.
+#4. Scan the one-minute waveform and select "spike maxima" whose amplitude exceeds a decibel threshold, D.
+#5. Extract a single frame (say 512 samples) centred on each spike and convert to a spike spectrum.
+#6. Subtract the noise profile from the spike spectrum.
+#7. Smooth the remaining spectrum.
+#8. Look for evenly spaced harmonics in the smoothed spectrum.
+#    Typically the lowest harmonic will lie between 1200 Hz and 3000 Hz and the higher ones evenly spaced.
+#    This is the tricky bit due to variability but may work to use spectrum auto-correlation.
+
+# Common settings
+BgNoiseThreshold: 3.0
+
+# Each of these profiles will be analyzed
+Profiles:
+  #Standard: &STANDARD
+  #EventThreshold: 0.2
+  Territorial:
+    # min and max of the freq band to search
+    MinHz: 800          
+    MaxHz: 8000
+    MinDuration: 0.15
+    MaxDuration: 0.8
+    DecibelThreshold: 9.0
+  Wingbeats:
+    MinHz: 200          
+    MaxHz: 2000
+    # duration of DCT in seconds 
+    DctDuration: 0.8
+    # minimum acceptable value of a DCT coefficient
+    DctThreshold: 0.5
+    # ignore oscillation rates below the min & above the max threshold
+    # A sample of four wingbeats yielded an average of 5.1 +/-0.5 beats/s.
+    # 95% confidence interval (2 SDs) is therefore approx 4-6 beats/s.    
+    # OSCILLATIONS PER SECOND
+    MinOscilFreq: 4        
+    MaxOscilFreq: 6
+    # Minimum and maximum duration for the length of a true call.
+    MinDuration: 1.0
+    MaxDuration: 10.0
+    # Event threshold - use this to determine FP / FN trade-off for events.
+    EventThreshold: 0.60
+  #Agonist:
+  # This notation means the Groote profile has all of the settings that the Standard profile has,
+  # however, the MinHz and MaxHz properties have been overridden.
+  #  <<: *STANDARD
+  #  DctDuration: 0.3
+
+# Resample rate must be 2 X the desired Nyquist
+ResampleRate: 22050
+
+## Specifically for AnalyzeLongRecording
+# SegmentDuration: units=seconds;    
+SegmentDuration: 60
+# SegmentOverlap: units=seconds;
+SegmentOverlap: 0
+# Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+SaveIntermediateWavFiles: Never
+SaveIntermediateCsvFiles: false
+# Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+# "True" is useful when debugging but "WhenEventsDetected" is required for operational use.
+# SaveSonogramImages: True
+SaveSonogramImages: WhenEventsDetected
+# DisplayCsvImage is obsolete - ensure it remains set to: false
+DisplayCsvImage: false
+## End section for AnalyzeLongRecording
+
+# Other config files to reference
+
+HighResolutionIndicesConfig: "../Towsey.Acoustic.HiResIndicesForRecognisers.yml"
+...

src/AnalysisPrograms/AnalysisPrograms.csproj

@@ -357,6 +357,7 @@
     <Compile Include="Recognizers\LitoriaWatjulumensis.cs" />
     <Compile Include="Recognizers\LitoriaBicolor.cs" />
     <Compile Include="Recognizers\PezoporusOccidentalis.cs" />
+    <Compile Include="Recognizers\PteropusSpecies.cs" />
     <Compile Include="Recognizers\UperoleiaLithomoda.cs" />
     <Compile Include="Recognizers\PlatyplectrumOrnatum.cs" />
     <Compile Include="Recognizers\LimnodynastesConvex.cs" />

src/AnalysisPrograms/Recognizers/LitoriaFallax.cs

@@ -1,4 +1,4 @@
-// --------------------------------------------------------------------------------------------------------------------
+// --------------------------------------------------------------------------------------------------------------------
 // <copyright file="LitoriaFallax.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>
@@ -201,7 +201,7 @@ private void WriteDebugImage(
             bool displayDebugImage = MainEntry.InDEBUG;
             if (displayDebugImage)
             {
-                Image debugImage1 = LitoriaRothii.DisplayDebugImage(sonogram, acousticEvents, plots, hits);
+                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits);
                 var debugPath1 =
                     outputDirectory.Combine(
                         FilenameHelpers.AnalysisResultName(
@@ -231,7 +231,7 @@ private void WriteDebugImage(
                             this.Identifier,
                             "png",
                             "DebugSpectrogram2"));
-                Image debugImage2 = LitoriaRothii.DisplayDebugImage(sonogram2, acousticEvents, plots, null);
+                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null);
                 debugImage2.Save(debugPath2.FullName);
             }
         }

src/AnalysisPrograms/Recognizers/LitoriaFreycineti.cs

@@ -1,4 +1,4 @@
-// --------------------------------------------------------------------------------------------------------------------
+// --------------------------------------------------------------------------------------------------------------------
 // <copyright file="LitoriaFreycineti.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>
@@ -195,7 +195,7 @@ private void WriteDebugImage(
             bool displayDebugImage = MainEntry.InDEBUG;
             if (displayDebugImage)
             {
-                Image debugImage1 = LitoriaRothii.DisplayDebugImage(sonogram, acousticEvents, plots, hits);
+                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits);
                 var debugPath1 =
                     outputDirectory.Combine(
                         FilenameHelpers.AnalysisResultName(
@@ -225,7 +225,7 @@ private void WriteDebugImage(
                             this.Identifier,
                             "png",
                             "DebugSpectrogram2"));
-                Image debugImage2 = LitoriaRothii.DisplayDebugImage(sonogram2, acousticEvents, plots, null);
+                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null);
                 debugImage2.Save(debugPath2.FullName);
             }
         }

src/AnalysisPrograms/Recognizers/LitoriaRothii.cs

@@ -1,4 +1,4 @@
-// --------------------------------------------------------------------------------------------------------------------
+// --------------------------------------------------------------------------------------------------------------------
 // <copyright file="LitoriaRothii.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>
@@ -223,7 +223,7 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
                 var lowPassPlot = new Plot("Low Pass", normalisedScores, normalisedThreshold);
 
                 var debugPlots = new List<Plot> { ampltdPlot, lowPassPlot, demeanedPlot, plot };
-                Image debugImage = DisplayDebugImage(sonogram, acousticEvents, debugPlots, null);
+                Image debugImage = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, debugPlots, null);
                 var debugPath = outputDirectory.Combine(FilenameHelpers.AnalysisResultName(Path.GetFileNameWithoutExtension(recording.BaseName), this.Identifier, "png", "DebugSpectrogram"));
                 debugImage.Save(debugPath.FullName);
             }
@@ -236,37 +236,5 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
                 Events = acousticEvents,
             };
         }
-
-        public static Image DisplayDebugImage(BaseSonogram sonogram, List<AcousticEvent> events, List<Plot> scores, double[,] hits)
-        {
-            var image = new Image_MultiTrack(sonogram.GetImage(doHighlightSubband: false, add1KHzLines: true, doMelScale: false));
-            image.AddTrack(ImageTrack.GetTimeTrack(sonogram.Duration, sonogram.FramesPerSecond));
-            if (scores != null)
-            {
-                foreach (var plot in scores)
-                {
-                    image.AddTrack(ImageTrack.GetNamedScoreTrack(plot.data, 0.0, 1.0, plot.threshold, plot.title)); //assumes data normalised in 0,1
-                }
-            }
-
-            if (hits != null)
-            {
-                image.OverlayRainbowTransparency(hits);
-            }
-
-            if (events.Count > 0)
-            {
-                // set colour for the events
-                foreach (AcousticEvent ev in events)
-                {
-                    ev.BorderColour = AcousticEvent.DefaultBorderColor;
-                    ev.ScoreColour = AcousticEvent.DefaultScoreColor;
-                }
-
-                image.AddEvents(events, sonogram.NyquistFrequency, sonogram.Configuration.FreqBinCount, sonogram.FramesPerSecond);
-            }
-
-            return image.GetImage();
-        }
     }
 }