Set up new Koala mark3 call recognizer.

Issue #500:
1: Set up new Koala mark3 call recognizer and associated test file.
2: Remove previous test file that was no longer needed.
3: Set up new config file for the test recording.
4: The test recording is temporary - just to get started.

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.PhascolarctosCinereusMark3.yml

@@ -8,46 +8,95 @@ SegmentDuration: 60
 # SegmentOverlap: units=seconds;
 SegmentOverlap: 0
 
+CommonParameters: &common_parameters
+    SpeciesName: PhascolarctosCinereus
+    WindowFunction: HANNING
+    NoiseReductionType: Standard
+    BgNoiseThreshold: 0.0
+
+
 # Each of these profiles will be analyzed
 Profiles:
+    # This profile detections oscillation in the inhale.
     KoalaOsc: !OscillationParameters
+        <<: *common_parameters
+
         ComponentName: Oscillation 
-        SpeciesName: PhascolarctosCinereus
         FrameSize: 512
         FrameStep: 256
-        WindowFunction: HANNING
-        BgNoiseThreshold: 0.0
         # min and max of the freq band to search
-        MinHertz: 250          
+        MinHertz: 200          
         MaxHertz: 800
         # Min and max durations for the length of a true event (seconds).
-        MinDuration: 0.5
-        MaxDuration: 2.5
+        MinDuration: 0.2
+        MaxDuration: 3.5
         # duration of DCT in seconds
         # this cannot be too long because the oscillations are not constant.
-        DctDuration: 0.30
+        #DctDuration: 0.30
+        DctDuration: 0.2
         # minimum acceptable amplitude of a DCT coefficient
         DctThreshold: 0.5
         # OSCILLATIONS PER SECOND: ignore oscillation rates below the min & above the max threshold
-        MinOcilFreq: 20
-        MaxOcilFreq: 55
+        MinOscillationFrequency: 20
+        MaxOscillationFrequency: 60
         # Event threshold - Determines FP / FN trade-off for events.
         EventThreshold: 0.2
+        DecibelThresholds:
+            - 6.0
+
+#################### POST-PROCESSING of EVENTS ###################
+
+PostProcessing:
+    PostProcessInDecibelGroups: false
+
+# # The following generic post-processing steps are determined by config settings.
+# # Step 1: Combine overlapping events - events derived from all profiles.
+# # Step 2: Combine possible syllable sequences and filter on excess syllable count.
+# # Step 3: Remove events whose bandwidth is too small or large.
+# # Step 4: Remove events that have excessive noise in their side-bands.
+
+#     # 1: Combine overlapping events
+    CombineOverlappingEvents: false
+
+    # 2: Combine possible syllable sequences
+#    SyllableSequence:
+#        SyllableStartDifference: 1.2
+#        SyllableHertzGap: 2400
+        # FilterSyllableSequence: true
+        # SyllableMaxCount: 3
+        # ExpectedPeriod: 0.1
+
+# #     # 3: Remove events whose duration lies outside 3 SDs of an expected value.
+#    Duration:
+#        ExpectedDuration: 2.5
+#        DurationStandardDeviation: 0.6
 
+#     # 4: Remove events whose bandwidth lies outside 3 SDs of an expected value.
+#  #   Bandwidth:
+#         ExpectedBandwidth: 280
+#         BandwidthStandardDeviation: 40
+
+#     # 5: Filter the events for excess activity in their sidebands, i.e. upper and lower buffer zones
+#     SidebandActivity:
+#         LowerHertzBuffer: 150
+#         UpperHertzBuffer: 400
+#         MaxAverageSidebandDecibels: 3.0
+    RemoveEnclosedEvents: false
 
 ################################################################################
-# Save intermediate file options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
-SaveIntermediateWavFiles: Never
-SaveIntermediateCsvFiles: false
 
-# Save spectrogram images: available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+# Options to save results files
+# Available options for saving spectrograms (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 # "True" is useful when debugging but "WhenEventsDetected" is required for operational use.
-SaveSonogramImages: True
+SaveSonogramImages: Always
 #SaveSonogramImages: WhenEventsDetected
 
+# Save intermediate file options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+SaveIntermediateWavFiles: Never
+SaveIntermediateCsvFiles: false
+
 # DisplayCsvImage is obsolete - ensure it remains set to: false
 DisplayCsvImage: false
-## End section for AnalyzeLongRecording
 
 # Other config files to reference
 IndexPropertiesConfig: ".\\IndexPropertiesConfig.yml"

src/AnalysisPrograms/Recognizers/PhascolarctosCinereusMark3.cs

@@ -4,18 +4,17 @@
 
 namespace AnalysisPrograms.Recognizers
 {
+    using System;
+    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.Indices;
     using AudioAnalysisTools.WavTools;
     using log4net;
-    using System;
-    using System.Collections.Generic;
-    using System.IO;
-    using System.Linq;
-    using System.Reflection;
-    using System.Text;
     using static AnalysisPrograms.Recognizers.GenericRecognizer;
 
     /// <summary>
@@ -77,14 +76,33 @@ internal class PhascolarctosCinereusMark3 : RecognizerBase
 
         public override string Author => "Towsey";
 
-        public override string SpeciesName => "PhascolarctosCinereus";
+        public override string SpeciesName => "PhascolarctosCinereusMark3";
 
-        public override string Description => "Detects male Koala bellows. This is Koala Mark 3";
+        public override string Description => "Detects male Koala bellows. This is Koala Recognizer, Mark 3";
 
         public override string CommonName => "Koala";
 
         public override Status Status => Status.InDevelopment;
 
+        public override AnalyzerConfig ParseConfig(FileInfo file)
+        {
+            RuntimeHelpers.RunClassConstructor(typeof(KoalaConfig3).TypeHandle);
+            var config = ConfigFile.Deserialize<KoalaConfig3>(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 OscillationParameters)
+            {
+                return config;
+            }
+
+            throw new ConfigFileException("Koala Recognizer Mark3 expects one and only one Oscillation algorithm.", file);
+        }
+
         /// <summary>
         /// This method is called once per segment. Segments are typically one-minute duration.
         /// </summary>

tests/Acoustics.Test/AnalysisPrograms/Recognizers/KoalaMark3Tests.cs

@@ -1,4 +1,4 @@
-// <copyright file="KoalaV3Tests.cs" company="QutEcoacoustics">
+// <copyright file="KoalaMark3Tests.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>
 
@@ -8,14 +8,17 @@ namespace Acoustics.Test.AnalysisPrograms.Recognizers
     using System.IO;
     using Acoustics.Test.TestHelpers;
     using global::AnalysisPrograms.Recognizers;
+    using global::AudioAnalysisTools;
+    using global::AudioAnalysisTools.Events;
     using global::AudioAnalysisTools.Events.Types;
     using global::AudioAnalysisTools.WavTools;
     using Microsoft.VisualStudio.TestTools.UnitTesting;
 
+    // [Ignore("Currently failing but also this work has not yet been implemented")]
+
     /// <summary>
     /// Species name = Koala = Botaurus poiciloptilus.
     /// Recognizer class = Phascolarctos cinereus.cs.
-    /// [Ignore("Currently failing but also this work has not yet been implemented")]
     /// </summary>
     [TestClass]
     public class KoalaMark3Tests : OutputDirectoryTest
@@ -26,7 +29,7 @@ public class KoalaMark3Tests : OutputDirectoryTest
         //private static readonly FileInfo TestAsset = PathHelper.ResolveAsset("Recordings", "koala.wav");
         private static readonly FileInfo TestAsset = new FileInfo("C:\\Ecoacoustics\\WavFiles\\KoalaMale\\Jackaroo_20080715-103940.wav");
         private static readonly FileInfo ConfigFile = PathHelper.ResolveConfigFile("RecognizerConfigFiles", "Towsey.PhascolarctosCinereusMark3.yml");
-        private static readonly PhascolarctosCinereus Recognizer = new PhascolarctosCinereus();
+        private static readonly PhascolarctosCinereusMark3 Recognizer = new PhascolarctosCinereusMark3();
 
         //NOTE: If testing recording at its original sample-rate, then use line below.
         //private static readonly AudioRecording Recording = new AudioRecording(TestAsset);
@@ -35,7 +38,7 @@ public class KoalaMark3Tests : OutputDirectoryTest
         //  as in the TestRecognizer() method below.
 
         [TestMethod]
-        public void TestRecognizer()
+        public void TestKoala3Recognizer()
         {
             var config = Recognizer.ParseConfig(ConfigFile);
             int resampleRate = config.ResampleRate.Value;
@@ -45,7 +48,7 @@ public void TestRecognizer()
 
             var results = Recognizer.Recognize(
                 audioRecording: recording,
-                config: config,
+                configuration: config,
                 segmentStartOffset: TimeSpan.Zero,
                 getSpectralIndexes: null,
                 outputDirectory: this.TestOutputDirectory,
@@ -59,21 +62,21 @@ public void TestRecognizer()
             this.SaveTestOutput(
                 outputDirectory => GenericRecognizer.SaveDebugSpectrogram(results, null, outputDirectory, Recognizer.SpeciesName));
 
-            Assert.AreEqual(1, events.Count);
+            Assert.AreEqual(12, events.Count);
             Assert.IsNull(scoreTrack);
-            Assert.AreEqual(1, plots.Count);
-            Assert.AreEqual(938, sonogram.FrameCount);
+            Assert.AreEqual(2, plots.Count);
+            //Assert.AreEqual(938, sonogram.FrameCount);
 
-            Assert.IsInstanceOfType(events[0], typeof(CompositeEvent));
+            Assert.IsInstanceOfType(events[0], typeof(OscillationEvent));
 
-            var onlyEvent = (CompositeEvent)events[0];
+            var ev = (SpectralEvent)events[0];
 
-            Assert.AreEqual(5.12, onlyEvent.EventStartSeconds);
-            Assert.AreEqual(12.26, onlyEvent.EventEndSeconds);
-            Assert.AreEqual(105, onlyEvent.LowFrequencyHertz);
-            Assert.AreEqual(180, onlyEvent.HighFrequencyHertz);
-            Assert.AreEqual(21.7, onlyEvent.Score);
-            Assert.AreEqual(0.95, onlyEvent.ScoreNormalized);
+            Assert.AreEqual(5.12, ev.EventStartSeconds);
+            Assert.AreEqual(12.26, ev.EventEndSeconds);
+            Assert.AreEqual(105, ev.LowFrequencyHertz);
+            Assert.AreEqual(180, ev.HighFrequencyHertz);
+            Assert.AreEqual(21.7, ev.Score);
+            Assert.AreEqual(0.95, ev.ScoreNormalized);
         }
     }
 }