Add new events filter

Issue #319 Add new post-processing event filter which filters depending on the number of component events in a composite event. Also change order of filters.

src/AnalysisPrograms/Recognizers/Birds/NinoxBoobook.cs

@@ -93,66 +93,48 @@ public override RecognizerResults Recognize(
                 imageWidth);
 
             // ################### DO POST-PROCESSING of EVENTS ###################
+            // Following two commented lines are different ways of casting lists.
+            //var newEvents = spectralEvents.Cast<EventCommon>().ToList();
+            //var spectralEvents = events.Select(x => (SpectralEvent)x).ToList();
 
-            // 1: Pull out the chirp events for possible combining.
+            // 1: Pull out the chirp events and calculate their frequency profiles.
             var (chirpEvents, others) = combinedResults.NewEvents.FilterForEventType<ChirpEvent, EventCommon>();
 
             // Uncomment the next line when want to obtain the event frequency profiles.
             // WriteFrequencyProfiles(chirpEvents);
 
-            // 2: Calculate frequency profile score for each event
             foreach (var ev in chirpEvents)
             {
+                // Calculate frequency profile score for event
                 SetFrequencyProfileScore((ChirpEvent)ev);
             }
 
-            // Following two commented lines are different ways of casting lists.
-            //var newEvents = spectralEvents.Cast<EventCommon>().ToList();
-            //var spectralEvents = events.Select(x => (SpectralEvent)x).ToList();
-
-            // 3: Combine overlapping events. If the dB threshold is set low, may get lots of little events.
-            var combinedEvents = CompositeEvent.CombineOverlappingEvents(chirpEvents.Cast<EventCommon>().ToList());
+            // 2: Combine overlapping events. If the dB threshold is set low, may get lots of little events.
+            combinedResults.NewEvents = CompositeEvent.CombineOverlappingEvents(chirpEvents.Cast<EventCommon>().ToList());
+            Console.WriteLine($"Event count after combining overlaps = {combinedResults.NewEvents.Count}");
 
-            // 4: Combine proximal events. If the dB threshold is set low, may get lots of little events.
+            // 3: Combine proximal events. If the dB threshold is set low, may get lots of little events.
             if (genericConfig.CombinePossibleSyllableSequence)
             {
                 // Convert events to spectral events for combining of possible sequences.
                 // Can also use this parameter to combine events that are in the upper or lower neighbourhood.
                 // Such combinations will increase bandwidth of the event and this property can be used later to weed out unlikely events.
-                var spectralEvents = combinedEvents.Cast<SpectralEvent>().ToList();
+                var spectralEvents1 = combinedResults.NewEvents.Cast<SpectralEvent>().ToList();
                 var startDiff = genericConfig.SyllableStartDifference;
                 var hertzDiff = genericConfig.SyllableHertzGap;
-                combinedEvents = CompositeEvent.CombineProximalEvents(spectralEvents, TimeSpan.FromSeconds(startDiff), (int)hertzDiff);
+                combinedResults.NewEvents = CompositeEvent.CombineProximalEvents(spectralEvents1, TimeSpan.FromSeconds(startDiff), (int)hertzDiff);
+                LoggedConsole.WriteLine($"Event count after combining proximals = {combinedResults.NewEvents.Count}");
             }
 
-            Console.WriteLine($"Event count after combining events = {combinedResults.NewEvents.Count}");
-
-            // 5: Filter the events for duration in seconds
+            // Get the BoobookSyllable config.
             var configuration = (GenericRecognizerConfig)genericConfig;
             var chirpConfig = (ForwardTrackParameters)configuration.Profiles["BoobookSyllable"];
-            var minimumEventDuration = chirpConfig.MinDuration;
-            var maximumEventDuration = chirpConfig.MaxDuration;
-            if (genericConfig.CombinePossibleSyllableSequence)
-            {
-                minimumEventDuration *= 2.0;
-                maximumEventDuration *= 1.5;
-            }
 
-            combinedResults.NewEvents = SpectralEvent.FilterOnDuration(combinedEvents, minimumEventDuration.Value, maximumEventDuration.Value);
-            Console.WriteLine($"Event count after filtering on duration = {combinedResults.NewEvents.Count}");
-
-            // 6: Filter the events for bandwidth in Hertz
-            double average = 280;
-            double sd = 40;
-            double sigmaThreshold = 3.0;
-            combinedResults.NewEvents = SpectralEvent.FilterOnBandwidth(combinedResults.NewEvents, average, sd, sigmaThreshold);
-            Console.WriteLine($"Event count after filtering on bandwidth = {combinedResults.NewEvents.Count}");
-
-            // 7: Finally, filter events on the amount of acoustic activity in their upper and lower neighbourhoods - their buffer zone.
+            // 4: Filter events on the amount of acoustic activity in their upper and lower neighbourhoods - their buffer zone.
             //    The idea is that an unambiguous event should have some acoustic space above and below.
-            //    Here it is assumed that the average acoustic activity in the upper and lower buffer zones should not exceed the user specified decibel threshold.
-            //    The size of the neighbourhood is determined by the following two parameters.
-            //    ################# These parameters should be specified by user in config.yml file.
+            //    The filter requires that the average acoustic activity in each frame and bin of the upper and lower buffer zones should not exceed the user specified decibel threshold.
+            //    The bandwidth of these two neighbourhoods is determined by the following parameters.
+            //    ########## These parameters could be specified by user in config.yml file.
             var upperHertzBuffer = 400;
             var lowerHertzBuffer = 150;
 
@@ -166,8 +148,34 @@ public override RecognizerResults Recognize(
                     upperHertzBuffer,
                     segmentStartOffset,
                     chirpConfig.DecibelThreshold.Value);
+
+                LoggedConsole.WriteLine($"Event count after filtering on neighbourhood = {combinedResults.NewEvents.Count}");
+            }
+
+            // 5: Filter on COMPONENT COUNT in Composite events.
+            int maxComponentCount = 2;
+            combinedResults.NewEvents = SpectralEvent.FilterEventsOnCompositeContent(combinedResults.NewEvents, maxComponentCount);
+            LoggedConsole.WriteLine($"Event count after filtering on component count = {combinedResults.NewEvents.Count}");
+
+            // 6: Filter the events for duration in seconds
+            var minimumEventDuration = chirpConfig.MinDuration;
+            var maximumEventDuration = chirpConfig.MaxDuration;
+            if (genericConfig.CombinePossibleSyllableSequence)
+            {
+                minimumEventDuration *= 2.0;
+                maximumEventDuration *= 1.5;
             }
 
+            combinedResults.NewEvents = SpectralEvent.FilterOnDuration(combinedResults.NewEvents, minimumEventDuration.Value, maximumEventDuration.Value);
+            LoggedConsole.WriteLine($"Event count after filtering on duration = {combinedResults.NewEvents.Count}");
+
+            // 7: Filter the events for bandwidth in Hertz
+            double average = 280;
+            double sd = 40;
+            double sigmaThreshold = 3.0;
+            combinedResults.NewEvents = SpectralEvent.FilterOnBandwidth(combinedResults.NewEvents, average, sd, sigmaThreshold);
+            LoggedConsole.WriteLine($"Event count after filtering on bandwidth = {combinedResults.NewEvents.Count}");
+
             //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 UserName.SpeciesName.yml config file.
             //GenericRecognizer.SaveDebugSpectrogram(territorialResults, genericConfig, outputDirectory, audioRecording.BaseName);

src/AudioAnalysisTools/Events/SpectralEvent.cs

@@ -10,6 +10,7 @@ namespace AudioAnalysisTools.Events
     using AnalysisBase.ResultBases;
     using AudioAnalysisTools.Events.Drawing;
     using AudioAnalysisTools.Events.Interfaces;
+    using AudioAnalysisTools.Events.Types;
     using AudioAnalysisTools.StandardSpectrograms;
     using SixLabors.ImageSharp;
     using SixLabors.ImageSharp.Processing;
@@ -198,8 +199,33 @@ public static List<EventCommon> FilterOnDuration(List<EventCommon> events, doubl
             int upperBinGap,
             UnitConverters converter)
         {
-            var subMatrix1 = GetUpperNeighbourhood(ev, sonogramData, upperHertzBuffer, upperBinGap, converter);
-            var subMatrix2 = GetLowerNeighbourhood(ev, sonogramData, lowerHertzBuffer, lowerBinGap, converter);
+            double[,] subMatrix1 = null;
+            if (upperHertzBuffer > 0)
+            {
+                subMatrix1 = GetUpperNeighbourhood(ev, sonogramData, upperHertzBuffer, upperBinGap, converter);
+            }
+
+            double[,] subMatrix2 = null;
+            if (upperHertzBuffer > 0)
+            {
+                subMatrix2 = GetLowerNeighbourhood(ev, sonogramData, lowerHertzBuffer, lowerBinGap, converter);
+            }
+
+            if (subMatrix1 == null && subMatrix2 == null)
+            {
+                return null;
+            }
+
+            if (subMatrix1 == null)
+            {
+                return subMatrix2;
+            }
+
+            if (subMatrix2 == null)
+            {
+                return subMatrix1;
+            }
+
             var matrix = MatrixTools.ConcatenateTwoMatrices(subMatrix1, subMatrix2);
             return matrix;
         }
@@ -315,5 +341,28 @@ public static List<EventCommon> FilterEventsOnNeighbourhood(
 
             return filteredEvents;
         }
+
+        /// <summary>
+        /// Removes composite events from a list of EventCommon that contain more than the specfied number of SpectralEvent components.
+        /// </summary>
+        public static List<EventCommon> FilterEventsOnCompositeContent(
+            List<EventCommon> events,
+            int maxComponentCount)
+        {
+            var filteredEvents = new List<EventCommon>();
+
+            foreach (var ev in events)
+            {
+                if (ev is CompositeEvent && ((CompositeEvent)ev).ComponentCount > maxComponentCount)
+                {
+                    // ignore composite events which contain more than the specified component events.
+                    continue;
+                }
+
+                filteredEvents.Add(ev);
+            }
+
+            return filteredEvents;
+        }
     }
 }

tests/Acoustics.Test/AnalysisPrograms/Recognizers/BoobookOwlTests.cs

@@ -26,7 +26,7 @@ public class BoobookOwlTests : OutputDirectoryTest
         /// <summary>
         /// The canonical recording used for this recognizer is a 31 second recording made by Yvonne Phillips at Gympie National Park, 2015-08-18.
         /// </summary>
-        private static readonly FileInfo TestAsset = PathHelper.ResolveAsset("Recordings", "gympie_np_1192_331618_20150818_054959_31_0.wav");        
+        private static readonly FileInfo TestAsset = PathHelper.ResolveAsset("Recordings", "gympie_np_1192_331618_20150818_054959_31_0.wav");
         private static readonly FileInfo ConfigFile = PathHelper.ResolveConfigFile("RecognizerConfigFiles", "Towsey.NinoxBoobook.yml");
         private static readonly AudioRecording Recording = new AudioRecording(TestAsset);
         private static readonly NinoxBoobook Recognizer = new NinoxBoobook();