Start work on Boobook recognizer

Issue #297 THis boobook recognizer is the first one which is species specific but extracts generic components and then does post-processing on the find primitive components.

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.NinoxBoobook.yml

@@ -0,0 +1,58 @@
+---
+
+# Resample rate must be 2 X the desired Nyquist
+#ResampleRate: 22050
+#ResampleRate: 16000
+# SegmentDuration: units=seconds;    
+SegmentDuration: 60
+# SegmentOverlap: units=seconds;
+SegmentOverlap: 0
+
+# Each of these profiles will be analyzed
+Profiles:
+    PeakTrackSyllable: !ForwardTrackParameters
+        ComponentName: RidgeTrack 
+        SpeciesName: NinoxBoobook
+        FrameSize: 1024
+        FrameStep: 256
+        WindowFunction: HANNING
+        BgNoiseThreshold: 0.0
+        # min and max of the freq band to search
+        MinHertz: 300          
+        MaxHertz: 1000
+        MinDuration: 0.15
+        MaxDuration: 0.5
+        DecibelThreshold: 6.0
+
+#Combine each pair of Boobook syllables as one event
+#CombineProximalSimilarEvents: false
+CombinePossibleSyllableSequence: true
+SyllableStartDifference: 0.6
+SyllableHertzGap: 200
+
+#CombineOverlappedEvents: false
+# Common settings
+#Standard: &STANDARD
+#EventThreshold: 0.2
+#BgNoiseThreshold: 3.0
+
+# This notation means the a profile has all of the settings that the Standard profile has,
+# however, the DctDuration parameter has been overridden.
+#  <<: *STANDARD
+#  DctDuration: 0.3
+
+# 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+# DisplayCsvImage is obsolete - ensure it remains set to: false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/Recognizers/Birds/NinoxBoobook.cs

@@ -2,34 +2,38 @@
 // 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>
-/// A recognizer for the Australian Boobook Owl, /// https://en.wikipedia.org/wiki/Australian_boobook .
-/// Eight subspecies of the Australian boobook are recognized,
-/// with three further subspecies being reclassified as separate species in 2019 due to their distinctive calls and genetics.
-/// THis recognizer has been trained on good quality calls from the Gympie recordings obtained by Yvonne Phillips.
-/// The recognizer has also been run across several recordings of Boobook from NZ (recordings obtained from Stuart Parsons.
-/// The NZ Boobook calls were of poor quality (distant and echo) and were 200 Hertz higher and performance was not good.
-/// </summary>
 namespace AnalysisPrograms.Recognizers
 {
     using System;
     using System.Collections.Generic;
     using System.IO;
     using System.Linq;
     using System.Reflection;
+    using System.Runtime.CompilerServices;
     using Acoustics.Shared.ConfigFile;
+    using AnalysisBase;
     using AnalysisPrograms.Recognizers.Base;
     using AudioAnalysisTools;
     using AudioAnalysisTools.DSP;
+    using AudioAnalysisTools.Events;
     using AudioAnalysisTools.Events.Types;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.StandardSpectrograms;
     using AudioAnalysisTools.WavTools;
     using log4net;
     using SixLabors.ImageSharp;
     using TowseyLibrary;
+    using static AnalysisPrograms.Recognizers.GenericRecognizer;
     using Path = System.IO.Path;
 
+    /// <summary>
+    /// A recognizer for the Australian Boobook Owl, /// https://en.wikipedia.org/wiki/Australian_boobook .
+    /// Eight subspecies of the Australian boobook are recognized,
+    /// with three further subspecies being reclassified as separate species in 2019 due to their distinctive calls and genetics.
+    /// THis recognizer has been trained on good quality calls from the Gympie recordings obtained by Yvonne Phillips.
+    /// The recognizer has also been run across several recordings of Boobook from NZ (recordings obtained from Stuart Parsons.
+    /// The NZ Boobook calls were of poor quality (distant and echo) and were 200 Hertz higher and performance was not good.
+    /// </summary>
     internal class NinoxBoobook : RecognizerBase
     {
         private static readonly ILog BoobookLog = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
@@ -40,113 +44,108 @@ internal class NinoxBoobook : RecognizerBase
 
         public override string Description => "[ALPHA] Detects acoustic events for the Australian Boobook owl.";
 
-        /*
-        /// <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)
+        public override AnalyzerConfig ParseConfig(FileInfo file)
         {
-            // No operation - do nothing. Feel free to add your own logic.
-            base.SummariseResults(settings, inputFileSegment, events, indices, spectralIndices, results);
+            RuntimeHelpers.RunClassConstructor(typeof(NinoxBoobookConfig).TypeHandle);
+            var config = ConfigFile.Deserialize<NinoxBoobookConfig>(file);
+
+            // validation of configs can be done here
+            GenericRecognizer.ValidateProfileTagsMatchAlgorithms(config.Profiles, file);
+
+            // This call sets a restriction so that only one generic algorithm is used.
+            // CHANGE this to accept multiple generic algorithms as required.
+            //if (result.Profiles.SingleOrDefault() is ForwardTrackParameters)
+            if (config.Profiles?.Count == 1 && config.Profiles.First().Value is ForwardTrackParameters)
+            {
+                return config;
+            }
+
+            throw new ConfigFileException("NinoxBoobook expects one and only one ForwardTrack algorithm.", file);
         }
-        */
 
         /// <summary>
         /// This method is called once per segment (typically one-minute segments).
         /// </summary>
         /// <param name="audioRecording">one minute of audio recording.</param>
-        /// <param name="genericConfig">config file that contains parameters used by all profiles.</param>
+        /// <param name="config">config file that contains parameters used by all profiles.</param>
         /// <param name="segmentStartOffset">when recording starts.</param>
         /// <param name="getSpectralIndexes">not sure what this is.</param>
         /// <param name="outputDirectory">where the recognizer results can be found.</param>
         /// <param name="imageWidth"> assuming ????.</param>
         /// <returns>recognizer results.</returns>
-        public override RecognizerResults Recognize(AudioRecording audioRecording, Config genericConfig, TimeSpan segmentStartOffset, Lazy<IndexCalculateResult[]> getSpectralIndexes, DirectoryInfo outputDirectory, int? imageWidth)
+        public override RecognizerResults Recognize(
+            AudioRecording audioRecording,
+            Config config,
+            TimeSpan segmentStartOffset,
+            Lazy<IndexCalculateResult[]> getSpectralIndexes,
+            DirectoryInfo outputDirectory,
+            int? imageWidth)
         {
+            //class NinoxBoobookConfig is define at bottom of this file.
+            var genericConfig = (NinoxBoobookConfig)config;
             var recognizer = new GenericRecognizer();
-            var config = recognizer.ParseConfig(FileInfo file);
 
-            /*
-            string[] profileNames = null;
-            if (ConfigFile.HasProfiles(genericConfig))
-            {
-                profileNames = ConfigFile.GetProfileNames(genericConfig);
-                int count = profileNames.Length;
-                var message = $"Found {count} config profile(s): ";
-                foreach (string s in profileNames)
-                {
-                    message = message + (s + ", ");
-                }
-
-                BoobookLog.Debug(message);
-            }
-            else
-            {
-                BoobookLog.Warn("No configuration profiles found.");
-            }
+            RecognizerResults combinedResults = recognizer.Recognize(
+                audioRecording,
+                genericConfig,
+                segmentStartOffset,
+                getSpectralIndexes,
+                outputDirectory,
+                imageWidth);
+
+            // DO POST-PROCESSING of EVENTS
 
-            var combinedResults = new RecognizerResults();
+            // Convert events to spectral events for possible combining.
+            // Combine overlapping events. If the dB threshold is set low, may get lots of little events.
+            //   
+            var events = combinedResults.NewEvents;
+            var spectralEvents = events.Select(x => (SpectralEvent)x).ToList();
+            var newEvents = CompositeEvent.CombineOverlappingEvents(spectralEvents);
 
-            foreach (var profileName in profileNames)
+            if (genericConfig.CombinePossibleSyllableSequence)
             {
-                var results = new RecognizerResults();
-
-                if (ConfigFile.TryGetProfile(genericConfig, profileName, out var profile))
-                {
-                    results = recognizer.(audioRecording, genericConfig, "Territorial", segmentStartOffset);
-                    BoobookLog.Debug("Boobook event count = " + results.Events.Count);
-                }
-                else
-                {
-                    BoobookLog.Warn($"Could not access {profileName} configuration parameters");
-                }
-
-                // combine the results i.e. add wing-beat events to the list of territorial call events.
-                //NOTE: The returned territorialResults and wingbeatResults will never be null.
-                combinedResults.Events.AddRange(results.Events);
-                combinedResults.Plots.AddRange(results.Plots);
+                // convert events to spectral events for possible combining.
+                //var spectralEvents = events.Select(x => (SpectralEvent)x).ToList();
+                spectralEvents = newEvents.Cast<SpectralEvent>().ToList();
+                var startDiff = genericConfig.SyllableStartDifference;
+                var hertzDiff = genericConfig.SyllableHertzGap;
+                newEvents = CompositeEvent.CombineSimilarProximalEvents(spectralEvents, TimeSpan.FromSeconds(startDiff), (int)hertzDiff);
             }
 
+            combinedResults.NewEvents = newEvents;
+
             //UNCOMMENT following line if you want special debug spectrogram, i.e. with special plots.
             //  NOTE: Standard spectrograms are produced by setting SaveSonogramImages: "True" or "WhenEventsDetected" in <Towsey.PteropusSpecies.yml> config file.
-            //SaveDebugSpectrogram(territorialResults, genericConfig, outputDirectory, audioRecording.BaseName);
-            */
+            //GenericRecognizer.SaveDebugSpectrogram(territorialResults, genericConfig, outputDirectory, audioRecording.BaseName);
             return combinedResults;
         }
 
+        /*
         /// <summary>
-        /// returns a base sonogram type from which spectrogram images are prepared.
+        /// Summarize your results. This method is invoked exactly once per original file.
         /// </summary>
-        internal static BaseSonogram GetSonogram(Config configuration, AudioRecording audioRecording)
+        public override void SummariseResults(
+            AnalysisSettings settings,
+            FileSegment inputFileSegment,
+            EventBase[] events,
+            SummaryIndexBase[] indices,
+            SpectralIndexBase[] spectralIndices,
+            AnalysisResult2[] results)
         {
-            var sonoConfig = new SonogramConfig
-            {
-                WindowSize = 512,
-                NoiseReductionType = NoiseReductionType.Standard,
-                NoiseReductionParameter = configuration.GetDoubleOrNull(AnalysisKeys.NoiseBgThreshold) ?? 0.0,
-                WindowOverlap = 0.0,
-            };
-
-            // now construct the standard decibel spectrogram WITH noise removal
-            // get frame parameters for the analysis
-            var sonogram = (BaseSonogram)new SpectrogramStandard(sonoConfig, audioRecording.WavReader);
-            return sonogram;
+            // No operation - do nothing. Feel free to add your own logic.
+            base.SummariseResults(settings, inputFileSegment, events, indices, spectralIndices, results);
         }
+        */
 
-        /// <summary>
-        /// THis method can be modified if want to do something non-standard with the output spectrogram.
-        /// </summary>
-        internal static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
+        /// <inheritdoc cref="NinoxBoobookConfig"/> />
+        public class NinoxBoobookConfig : GenericRecognizerConfig, INamedProfiles<object>
         {
-            //var image = sonogram.GetImageFullyAnnotated("Test");
-            var image = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.Events, results.Plots, null);
-            image.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
+            //public bool CombineOverlappedEvents { get; set; }
+            public bool CombinePossibleSyllableSequence { get; set; } = false;
+
+            public double SyllableStartDifference { get; set; } = 0.5;
+
+            public double SyllableHertzGap { get; set; } = 200;
         }
     }
 }

src/AnalysisPrograms/Recognizers/GenericRecognizer.cs

@@ -51,11 +51,17 @@ public override AnalyzerConfig ParseConfig(FileInfo file)
             RuntimeHelpers.RunClassConstructor(typeof(GenericRecognizerConfig).TypeHandle);
             var result = ConfigFile.Deserialize<GenericRecognizerConfig>(file);
 
-            this.combineOverlappedEvents = result.CombineOverlappedEvents;
+            // validation of configs can be done here
+            ValidateProfileTagsMatchAlgorithms(result.Profiles, file);
+
+            return result;
+        }
 
+        public static void ValidateProfileTagsMatchAlgorithms(Dictionary<string, object> profiles, FileInfo file)
+        {
             // validation of configs can be done here
             // sanity check the algorithm
-            foreach (var (profileName, profile) in result.Profiles)
+            foreach (var (profileName, profile) in profiles)
             {
                 if (profile is CommonParameters c)
                 {
@@ -103,8 +109,6 @@ public override AnalyzerConfig ParseConfig(FileInfo file)
                         throw new ConfigFileException($"The algorithm type in profile {profileName} is not recognized. It must be one of {allowedAlgorithms}");
                 }
             }
-
-            return result;
         }
 
         /// <inheritdoc/>
@@ -118,7 +122,7 @@ public override RecognizerResults Recognize(
         {
             var configuration = (GenericRecognizerConfig)genericConfig;
 
-            if (configuration.Profiles.NotNull() && configuration.Profiles.Count == 0)
+            if (configuration.Profiles?.Count < 1)
             {
                 throw new ConfigFileException(
                     "The generic recognizer needs at least one profile set. 0 were found.");
@@ -358,19 +362,14 @@ public override void SummariseResults(
         }
         */
 
-        private static SonogramConfig ParametersToSonogramConfig(CommonParameters common)
+        /// <summary>
+        /// THis method can be modified if want to do something non-standard with the output spectrogram.
+        /// </summary>
+        public static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
         {
-            int windowSize = (int)common.FrameSize;
-            int windowStep = (int)common.FrameStep;
-            return new SonogramConfig()
-            {
-                WindowSize = windowSize,
-                WindowStep = windowStep,
-                WindowOverlap = (windowSize - windowStep) / (double)windowSize,
-                WindowFunction = (string)common.WindowFunction,
-                NoiseReductionType = NoiseReductionType.Standard,
-                NoiseReductionParameter = common.BgNoiseThreshold ?? 0.0,
-            };
+            var image3 = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.NewEvents, results.Plots, null);
+
+            image3.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
         }
 
         /// <summary>
@@ -390,21 +389,24 @@ private static Plot PreparePlot(double[] array, string title, double threshold)
             return plot;
         }
 
-        /// <summary>
-        /// THis method can be modified if want to do something non-standard with the output spectrogram.
-        /// </summary>
-        public static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
+        private static SonogramConfig ParametersToSonogramConfig(CommonParameters common)
         {
-            var image3 = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.NewEvents, results.Plots, null);
-
-            image3.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
+            int windowSize = (int)common.FrameSize;
+            int windowStep = (int)common.FrameStep;
+            return new SonogramConfig()
+            {
+                WindowSize = windowSize,
+                WindowStep = windowStep,
+                WindowOverlap = (windowSize - windowStep) / (double)windowSize,
+                WindowFunction = (string)common.WindowFunction,
+                NoiseReductionType = NoiseReductionType.Standard,
+                NoiseReductionParameter = common.BgNoiseThreshold ?? 0.0,
+            };
         }
 
-        /// <inheritdoc cref="RecognizerConfig"/> />
+        /// <inheritdoc cref="GenericRecognizerConfig"/> />
         public class GenericRecognizerConfig : RecognizerConfig, INamedProfiles<object>
         {
-            public bool CombineOverlappedEvents { get; set; }
-
             /// <inheritdoc />
             public Dictionary<string, object> Profiles { get; set; }
         }