Set up Flying Fox Recogniser classes

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.PteropusSpecies.yml

@@ -0,0 +1,81 @@
+---
+# Should be in proper casing. The full real name of the species
+SpeciesName: Pteropus species
+CommonName: Flying Fox
+# Abbreviation of species name, format how you like
+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.
+
+# Custom settings
+
+SomeExampleSettingA: 3.0
+
+# Each of these profiles will be analyzed
+Profiles:
+  # The below settings are a template
+  Standard: &STANDARD
+    # min and max of the freq band to search
+    MinHz: 3000          
+    MaxHz: 5000
+    # duration of DCT in seconds 
+    DctDuration: 0.15
+    # minimum acceptable value of a DCT coefficient
+    DctThreshold: 0.6
+    # ignore oscillation rates below the min & above the max threshold
+    # OSCILLATIONS PER SECOND
+    MinOcilFreq: 50        
+    MaxOcilFreq: 140
+    # Minimum and maximum duration for the length of a true call.
+    MinDuration: 0.1
+    MaxDuration: 0.8
+    # Event threshold - use this to determine FP / FN trade-off for events.
+    EventThreshold: 0.30
+  # 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.
+  #Groote:
+  #  <<: *STANDARD
+  #  MinHz: 4000          
+  #  MaxHz: 6000
+  #FemaleRelease:
+  #  <<: *STANDARD
+  #  DctDuration: 0.3
+
+# Standard settings
+DoNoiseReduction: false
+#BgNoiseThreshold: 3.0
+
+EventThreshold: 0.2
+
+# Resample rate must be 2 X the desired Nyquist
+# ResampleRate: 17640
+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]
+SaveSonogramImages: Never
+# 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

@@ -358,6 +358,7 @@
     <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/PteropusSpecies.cs

@@ -0,0 +1,243 @@
+// --------------------------------------------------------------------------------------------------------------------
+// <copyright file="PteropusSpecies.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>
+// <summary>
+//   This is a template recognizer for the Australian Flying Fox.
+//   Since there are several species, this project is started using only the generic name for Flying Foxes.
+
+// Proposed algorithm has 8 steps
+// 1. Break long recordings into one-minute segments.
+// 2. Convert each 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 auto-correlation.
+// </summary>
+// --------------------------------------------------------------------------------------------------------------------
+
+namespace AnalysisPrograms.Recognizers
+{
+    using System;
+    using System.Collections.Generic;
+    using System.IO;
+    using System.Linq;
+    using System.Reflection;
+    using System.Text;
+    using Acoustics.Shared.ConfigFile;
+    using Acoustics.Tools.Wav;
+    using AnalysisBase;
+    using AnalysisBase.ResultBases;
+    using AnalysisPrograms.Recognizers.Base;
+    using AudioAnalysisTools;
+    using AudioAnalysisTools.DSP;
+    using AudioAnalysisTools.Indices;
+    using AudioAnalysisTools.StandardSpectrograms;
+    using AudioAnalysisTools.WavTools;
+    using log4net;
+    using TowseyLibrary;
+
+    /// <summary>
+    /// This is a template recognizer for species of Flying Fox, Pteropus species
+    /// </summary>
+    internal class PteropusSpecies : RecognizerBase
+    {
+        public override string Author => "Truskinger";
+
+        public override string SpeciesName => "PteropusSpecies";
+
+        public override string Description => "[STATUS DESCRIPTION] Detects acoustic events for species of Flying Fox, Pteropus species";
+
+        private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
+
+        /// <summary>
+        /// Summarize your results. This method is invoked exactly once per original file.
+        /// </summary>
+        public override void SummariseResults(
+            AnalysisSettings settings,
+            FileSegment inputFileSegment,
+            EventBase[] events,
+            SummaryIndexBase[] indices,
+            SpectralIndexBase[] spectralIndices,
+            AnalysisResult2[] results)
+        {
+            // No operation - do nothing. Feel free to add your own logic.
+            base.SummariseResults(settings, inputFileSegment, events, indices, spectralIndices, results);
+        }
+
+        /// <summary>
+        /// Do your analysis. This method is called once per segment (typically one-minute segments).
+        /// </summary>
+        /// <param name="audioRecording">one minute of audio recording.</param>
+        /// <param name="configuration">config file.</param>
+        /// <param name="segmentStartOffset">when recording starts.</param>
+        /// <param name="getSpectralIndexes">not sure what this is.</param>
+        /// <param name="outputDirectory">where the recogniser results can be found.</param>
+        /// <param name="imageWidth"> assuming ????.</param>
+        /// <returns>recogniser results.</returns>
+        public override RecognizerResults Recognize(AudioRecording audioRecording, Config configuration, TimeSpan segmentStartOffset, Lazy<IndexCalculateResult[]> getSpectralIndexes, DirectoryInfo outputDirectory, int? imageWidth)
+        {
+            // Get a value from the config file - with a backup default
+            int minHz = configuration.GetIntOrNull(AnalysisKeys.MinHz) ?? 600;
+
+            // Get a value from the config file - with no default, throw an exception if value is not present
+            //int maxHz = ((int?)configuration[AnalysisKeys.MaxHz]).Value;
+
+            // Get a value from the config file - without a string accessor, as a double
+            double someExampleSettingA = configuration.GetDoubleOrNull("SomeExampleSettingA") ?? 0.0;
+
+            // common properties
+            string speciesName = configuration[AnalysisKeys.SpeciesName] ?? "<no species>";
+            string abbreviatedSpeciesName = configuration[AnalysisKeys.AbbreviatedSpeciesName] ?? "<no.sp>";
+
+            /*
+             * Examples of using profiles
+             */
+
+            // Examples of the APIs available. You don't need all of these commands! Pick and choose.
+            bool hasProfiles = ConfigFile.HasProfiles(configuration);
+
+            //Config profile = ConfigFile.GetProfile<Config, Aed.AedConfiguration>(configuration, "Groote");
+            Config profile2;
+
+            //bool success = ConfigFile.TryGetProfile(configuration, "FemaleRelease", out profile2);
+            //string[] profileNames = ConfigFile.GetProfileNames<Config>(configuration);
+            //            IEnumerable<(string Name, object Profile)> allProfiles = ConfigFile.GetAllProfiles<IProfile<object>>(configuration);
+            //            foreach (var profile in allProfiles)
+            //            {
+            //                object currentProfile = profile.Profile;
+            //                Log.Info(profile.Name + ": " + ((int)currentProfile.MinHz).ToString());
+            //            }
+
+            //######################
+            //2.Convert each segment to a spectrogram.
+
+            // Profile example: running the same algorithm on every profile with different settings (regional variation)
+            /*
+            List<AcousticEvent> allAcousticEvents = new List<AcousticEvent>();
+            Dictionary<string, Config> allProfiles = ConfigFile.GetAllProfiles(configuration);
+            foreach (var kvp in allProfiles)
+            {
+                string profileName = kvp.Key;
+                Log.Info($"Analyzing profile: {profileName}");
+                Config currentProfile = kvp.Value;
+
+                // extract parameters
+                int minHz = (int)configuration[AnalysisKeys.MinHz];
+
+                // ...
+
+                // run the algorithm
+                List<AcousticEvent> acousticEvents;
+                Oscillations2012.Execute( All the correct parameters, minHz);
+
+                // augment the returned events
+                acousticEvents.ForEach(ae =>
+                {
+                    ae.SpeciesName = speciesName;
+                    ae.Profile = profileName;
+                    ae.AnalysisIdealSegmentDuration = recordingDuration;
+                    ae.Name = abbreviatedSpeciesName;
+                });
+
+                // add events found in this profile to the total list
+                allAcousticEvents.AddRange(acousticEvents);
+            }
+            */
+
+            // Profile example: running a different algorithm on different profiles
+            /*
+            bool hasProfiles = ConfigFile.HasProfiles(configuration);
+            if (hasProfiles)
+            {
+                // add resulting events from each algorithm into the combined event list
+                allAcousticEvents.AddRange(RunFemaleProfile(...all the arguments));
+                allAcousticEvents.AddRange(RunMaleProfile(...all the arguments));
+            }
+
+            // example method
+            private static List<AcousticEvent> RunFemaleProfile(configuration, rest of arguments)
+            {
+                const string femaleProfile = "Female";
+                Config currentProfile = ConfigFile.GetProfile(configuration, femaleProfile);
+                Log.Info($"Analyzing profile: {femaleProfile}");
+
+                // extract parameters
+                int minHz = (int)configuration[AnalysisKeys.MinHz];
+
+                // ...
+
+                // run the algorithm
+                List<AcousticEvent> acousticEvents;
+                Oscillations2012.Execute(All the correct parameters, minHz);
+
+                // augment the returned events
+                acousticEvents.ForEach(ae =>
+                {
+                    ae.SpeciesName = speciesName;
+                    ae.Profile = femaleProfile;
+                    ae.AnalysisIdealSegmentDuration = recordingDuration;
+                    ae.Name = abbreviatedSpeciesName;
+                });
+
+                return acousticEvents;
+            }
+            */
+
+            // get samples
+            var samples = audioRecording.WavReader.Samples;
+
+            // make a spectrogram
+            var config = new SonogramConfig
+            {
+                NoiseReductionType = NoiseReductionType.Standard,
+                NoiseReductionParameter = configuration.GetDoubleOrNull(AnalysisKeys.NoiseBgThreshold) ?? 0.0,
+            };
+            var sonogram = (BaseSonogram)new SpectrogramStandard(config, audioRecording.WavReader);
+
+            // get high resolution indices
+
+            // when the value is accessed, the indices are calculated
+            var indices = getSpectralIndexes.Value;
+
+            // check if the indices have been calculated - you shouldn't actually need this
+            if (getSpectralIndexes.IsValueCreated)
+            {
+                // then indices have been calculated before
+            }
+
+            var foundEvents = new List<AcousticEvent>();
+
+            // some kind of loop where you scan through the audio
+
+            // 'find' a Flying Fox event - if you find an event, store the data in the AcousticEvent class
+            var anEvent = new AcousticEvent(
+                segmentStartOffset,
+                new Oblong(50, 50, 100, 100),
+                sonogram.NyquistFrequency,
+                sonogram.Configuration.FreqBinCount,
+                sonogram.FrameDuration,
+                sonogram.FrameStep,
+                sonogram.FrameCount)
+            {
+                Name = "Flying Fox",
+            };
+
+            foundEvents.Add(anEvent);
+
+            return new RecognizerResults()
+            {
+                Events = foundEvents,
+                Hits = null,
+                ScoreTrack = null,
+
+                //Plots = null,
+                Sonogram = sonogram,
+            };
+        }
+    }
+}

src/AnalysisPrograms/Sandpit.cs

@@ -276,6 +276,11 @@ public static void Audio2CsvOverOneFile()
             //FOR  MULTI-ANALYSER and CROWS
             //audio2csv  "C:\SensorNetworks\WavFiles\KoalaMale\SmallTestSet\DaguilarGoldCreek1_DM420157_0000m_00s__0059m_47s_49h.mp3" "C:\SensorNetworks\Software\AudioAnalysis\AnalysisConfigFiles\Towsey.MultiAnalyser.cfg" "C:\SensorNetworks\Output\Test1"
 
+            // FLYING FOX RECORDINGS
+            string recordingPath = @"C:\SensorNetworks\WavFiles\TsheringDema\WBH12HOURS-D_20160403_120000.wav";
+            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\RecognizerConfigFiles\Towsey.PteropusSpecies.yml";
+            string outputPath = @"C:\Ecoacoustics\Output\BradLaw\FlyingFox";
+
             // TSHERING DEMA BHUTAN RECORDINGS
             //string recordingPath = @"C:\SensorNetworks\WavFiles\TsheringDema\WBH12HOURS-D_20160403_120000.wav";
             //    @"Y:\Tshering\WBH_Walaytar\201505 - second deployment\Site2_Waklaytar\24Hours WBH_28032016\WBH12HOURS-D_20160403_120000.wav";
@@ -290,7 +295,6 @@ public static void Audio2CsvOverOneFile()
             //string recordingPath = @"G:\SensorNetworks\WavFiles\Bhutan\SecondDeployment\WBH12HOURS-N_20160403_000000.wav";
             //string outputPath = @"C:\SensorNetworks\Output\TsheringDema";
             //string configPath = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Acoustic.yml";
-
             // string configPath = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\RecognizerConfigFiles\Towsey.ArdeaInsignis.yml";
 
             //MARINE
@@ -326,10 +330,10 @@ public static void Audio2CsvOverOneFile()
             //string configPath = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
             // Test on STANDARD 24-HOUR RECORDING
-            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652.wav";
+            //string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652.wav";
             //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\14";
-            string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\Delete";
-            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
+            //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\Delete";
+            //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
             // Ivan Campos recordings
             //string recordingPath = @"G:\SensorNetworks\WavFiles\Ivancampos\INCIPO01_20161031_024006_898.wav";