Stub out initial recogniser files for NSW DPI project

Also added a generic recogniser template snippet that helps generate the boiler plate.

src/Acoustics.Shared/Meta.cs

@@ -25,20 +25,16 @@ public static class Meta
 
         private static Assembly[] ourAssemblies;
 
-        public static string BinaryName(bool isSelfContained)
-        {
-            var extension = isSelfContained ? string.Empty : ".dll";
-            return AppConfigHelper.IsWindows ? Name : "AnalysisPrograms" + extension;
-        }
-
         public static string Organization { get; } = "QUT";
 
-        public static string Website { get; } = "http://research.ecosounds.org/";
+        public static string Website { get; } = "https://ap.qut.ecoacoustics.info/";
 
         public static string OrganizationTag => CopyrightSymbol + " " + NowYear + " " + Organization;
 
         public static string Repository { get; } = "https://github.com/QutBioacoustics/audio-analysis";
 
+        public static string DebuggingHelp => GetDocsUrl("technical/debugging.html");
+
         internal static Assembly[] QutAssemblies
         {
             get
@@ -64,9 +60,15 @@ internal static Assembly[] QutAssemblies
             }
         }
 
+        public static string BinaryName(bool isSelfContained)
+        {
+            var extension = isSelfContained ? string.Empty : ".dll";
+            return AppConfigHelper.IsWindows ? Name : "AnalysisPrograms" + extension;
+        }
+
         public static string GetDocsUrl(string page)
         {
-            return $"{Repository}/blob/master/docs/{page}";
+            return $"{Website}/{page}";
         }
 
         public static IEnumerable<TypeInfo> GetTypesFromQutAssemblies<T>()

src/AnalysisBase/Citation.cs

@@ -0,0 +1,48 @@
+// <copyright file="Citation.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>
+
+namespace AnalysisBase
+{
+    using System;
+    using System.Collections.Generic;
+    using Acoustics.Shared;
+
+    public record Citation(IReadOnlyCollection<Author> Authors, string Title, string Project, string Uri);
+
+    public record Author(string FirstName, string LastName, string Affiliation, params string[] OtherNames);
+
+    public interface ICiteable
+    {
+        public IReadOnlyCollection<Citation> Citations => Array.Empty<Citation>();
+    }
+
+    public static class Bibliography
+    {
+        public static Author Anthony => new Author("Anthony", "Truskinger", "QUT Ecoacoustics");
+
+        public static Author Michael => new Author("Michael", "Towsey", "QUT Ecoacoustics");
+
+        public static Author Paul => new Author("Paul", "Roe", "QUT Ecoacoustics");
+
+        public static Author Kristen => new Author("Kristen", "Thompson", "NSW DPI");
+
+        public static Author Brad => new Author("Brad", "Law", "NSW DPI");
+
+        public static IReadOnlyCollection<Author> BuiltByAnthony => new[] { Anthony, Kristen, Michael, Paul, Brad };
+
+        public static IReadOnlyCollection<Author> BuiltByMichael => new[] { Michael, Kristen, Anthony, Paul, Brad };
+
+        public static Citation NswDpiRecognisersProject => new Citation(
+            Array.Empty<Author>(),
+            string.Empty,
+            "Recogniser project with NSW DPI: grant xxxx",
+            string.Empty);
+
+        public static Citation QutEcoacousticsProject => new Citation(
+            Array.Empty<Author>(),
+            string.Empty,
+            $"Recognizers devdeloped for various projects by {Meta.GroupName}",
+            Meta.Website);
+    }
+}

src/AnalysisBase/IAnalyser2.cs

@@ -24,7 +24,7 @@ namespace AnalysisBase
     /// This is a strong typed version of <c>IAnalyser</c> intentionally removed from the old inheritance tree.
     /// DO NOT MODIFY THIS FILE UNLESS INSTRUCTED TO!.
     /// </summary>
-    public interface IAnalyser2
+    public interface IAnalyser2 : ICiteable, IHasStatus
     {
         /// <summary>
         /// Gets the name to display for the analysis.

src/AnalysisBase/IHasStatus.cs

@@ -0,0 +1,18 @@
+// --------------------------------------------------------------------------------------------------------------------
+// <copyright file="IAnalyser2.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>
+//   Interface a compatible analysis must implement.
+//   This is a strong typed version of <c>IAnalyser</c> intentionally removed from the old inheritance tree.
+//   DO NOT MODIFY THIS FILE UNLESS INSTRUCTED TO!
+// </summary>
+// --------------------------------------------------------------------------------------------------------------------
+
+namespace AnalysisBase
+{
+    public interface IHasStatus
+    {
+        public Status Status => Status.Unknown;
+    }
+}

src/AnalysisBase/Status.cs

@@ -0,0 +1,24 @@
+// --------------------------------------------------------------------------------------------------------------------
+// <copyright file="IAnalyser2.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>
+//   Interface a compatible analysis must implement.
+//   This is a strong typed version of <c>IAnalyser</c> intentionally removed from the old inheritance tree.
+//   DO NOT MODIFY THIS FILE UNLESS INSTRUCTED TO!
+// </summary>
+// --------------------------------------------------------------------------------------------------------------------
+
+namespace AnalysisBase
+{
+    public enum Status
+    {
+        Unknown = 0,
+        InDevelopment,
+        Alpha,
+        Beta,
+        Maintained,
+        Unmaintained,
+        Retired,
+    }
+}

src/AnalysisPrograms/Production/MainEntryUtilities.cs

@@ -132,7 +132,7 @@ internal static void AttachDebugger(DebugOptions options)
                     var prompt =
 $@"Do you wish to debug?
     Attach now or press [Y] and [ENTER] to attach. Press [N] or [ENTER] to continue.
-See {Meta.GetDocsUrl("debugging.md")} for help.";
+See {Meta.DebuggingHelp} for help.";
 
                     var response = Prompt.GetYesNo(
                         prompt,

src/AnalysisPrograms/Recognizers/Base/RecognizerBase.cs

@@ -31,27 +31,12 @@ namespace AnalysisPrograms.Recognizers.Base
 
     public abstract class RecognizerBase : AbstractStrongAnalyser, IEventRecognizer
     {
-        public class RecognizerConfig : AnalyzerConfig
-        {
-            public RecognizerConfig()
-            {
-                this.Loaded += config =>
-                    {
-                        var file = ConfigFile.Resolve(this.HighResolutionIndicesConfig ?? "Towsey.Acoustic.HiResIndicesForRecognisers.yml");
-                        var indicesConfig = ConfigFile.Deserialize<AcousticIndices.AcousticIndicesConfig>(file);
-                        this.HighResolutionIndices = indicesConfig;
-                    };
-            }
-
-            public string HighResolutionIndicesConfig { get; set; }
-
-            public AcousticIndices.AcousticIndicesConfig HighResolutionIndices { get; private set; }
-        }
-
         public abstract string Author { get; }
 
         public abstract string SpeciesName { get; }
 
+        public abstract string CommonName { get; }
+
         public override string Identifier => this.Author + "." + this.SpeciesName;
 
         public override string DisplayName => this.SpeciesName;
@@ -65,6 +50,42 @@ public RecognizerConfig()
             AnalysisTargetSampleRate = AppConfigHelper.DefaultTargetSampleRate,
         };
 
+        public static Image<Rgb24> DrawDebugImage(BaseSonogram sonogram, List<AcousticEvent> events, List<Plot> scores, double[,] hits)
+        {
+            const bool doHighlightSubband = false;
+            const bool add1KHzLines = true;
+            var image = new Image_MultiTrack(sonogram.GetImage(doHighlightSubband, add1KHzLines, doMelScale: false));
+
+            image.AddTrack(ImageTrack.GetTimeTrack(sonogram.Duration, sonogram.FramesPerSecond));
+            if (scores != null)
+            {
+                foreach (var plot in scores)
+                {
+                    // assumes data normalised in 0,1
+                    image.AddTrack(ImageTrack.GetNamedScoreTrack(plot.data, 0.0, 1.0, plot.threshold, plot.title));
+                }
+            }
+
+            if (hits != null)
+            {
+                image.OverlayRainbowTransparency(hits);
+            }
+
+            if (events.Count > 0)
+            {
+                // set colour for the events
+                foreach (var ev in events)
+                {
+                    ev.BorderColour = AcousticEvent.DefaultBorderColor;
+                    ev.ScoreColour = AcousticEvent.DefaultScoreColor;
+                }
+
+                image.AddEvents(events, sonogram.NyquistFrequency, sonogram.Configuration.FreqBinCount, sonogram.FramesPerSecond);
+            }
+
+            return image.GetImage().CloneAs<Rgb24>();
+        }
+
         public override AnalyzerConfig ParseConfig(FileInfo file)
         {
             return ConfigFile.Deserialize<RecognizerConfig>(file);
@@ -411,38 +432,21 @@ IndexCalculateResult[] Callback()
             return new Lazy<IndexCalculateResult[]>(Callback, LazyThreadSafetyMode.ExecutionAndPublication);
         }
 
-        public static Image<Rgb24> DrawDebugImage(BaseSonogram sonogram, List<AcousticEvent> events, List<Plot> scores, double[,] hits)
+        public class RecognizerConfig : AnalyzerConfig
         {
-            const bool doHighlightSubband = false;
-            const bool add1KHzLines = true;
-            var image = new Image_MultiTrack(sonogram.GetImage(doHighlightSubband, add1KHzLines, doMelScale: false));
-
-            image.AddTrack(ImageTrack.GetTimeTrack(sonogram.Duration, sonogram.FramesPerSecond));
-            if (scores != null)
+            public RecognizerConfig()
             {
-                foreach (var plot in scores)
+                this.Loaded += config =>
                 {
-                    image.AddTrack(ImageTrack.GetNamedScoreTrack(plot.data, 0.0, 1.0, plot.threshold, plot.title)); //assumes data normalised in 0,1
-                }
+                    var file = ConfigFile.Resolve(this.HighResolutionIndicesConfig ?? "Towsey.Acoustic.HiResIndicesForRecognisers.yml");
+                    var indicesConfig = ConfigFile.Deserialize<AcousticIndices.AcousticIndicesConfig>(file);
+                    this.HighResolutionIndices = indicesConfig;
+                };
             }
 
-            if (hits != null)
-            {
-                image.OverlayRainbowTransparency(hits);
-            }
-
-            if (events.Count > 0)
-            {
-                foreach (var ev in events) // set colour for the events
-                {
-                    ev.BorderColour = AcousticEvent.DefaultBorderColor;
-                    ev.ScoreColour = AcousticEvent.DefaultScoreColor;
-                }
-
-                image.AddEvents(events, sonogram.NyquistFrequency, sonogram.Configuration.FreqBinCount, sonogram.FramesPerSecond);
-            }
+            public string HighResolutionIndicesConfig { get; set; }
 
-            return image.GetImage().CloneAs<Rgb24>();
+            public AcousticIndices.AcousticIndicesConfig HighResolutionIndices { get; private set; }
         }
     }
 }

src/AnalysisPrograms/Recognizers/Birds/NinoxConnivens.cs

@@ -0,0 +1,85 @@
+// <copyright file="NinoxConnivens.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>
+
+namespace AnalysisPrograms.Recognizers.Birds
+{
+    using System;
+    using System.Collections.Generic;
+    using System.IO;
+    using System.Reflection;
+    using System.Runtime.CompilerServices;
+    using System.Text;
+    using Acoustics.Shared.ConfigFile;
+    using AnalysisBase;
+    using AnalysisPrograms.Recognizers.Base;
+    using AudioAnalysisTools.Indices;
+    using AudioAnalysisTools.WavTools;
+    using log4net;
+
+    /// <summary>
+    /// A recognizer for the Barking Owl, https://en.wikipedia.org/wiki/Barking_owl.
+    /// The barking owl (Ninox connivens), also known as the winking owl, is a nocturnal bird species native to mainland Australia
+    /// and partsof Papua New Guinea and the Moluccas. They are a medium-sized brown owl and have a characteristic voice with
+    /// calls ranging from a barking dog noise to a shrill human-like howl of great intensity.
+    /// This recognizer has been trained on good quality calls provided by NSW DPI by Brad Law and Kristen Thompson.
+    /// </summary>
+    public class NinoxConnivens : RecognizerBase
+    {
+        private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
+
+        public override string Author => Bibliography.Anthony.LastName;
+
+        public override string SpeciesName => "NinoxConnivens";
+
+        public override string CommonName => "Barking owl";
+
+        public Status Status => Status.InDevelopment;
+
+        public override string Description => $"Acoustic event recognizer for the {this.CommonName}.";
+
+        public IReadOnlyCollection<Citation> Citations => new[] {
+            Bibliography.NswDpiRecognisersProject with {
+                Authors = Bibliography.BuiltByAnthony,
+                Title = this.Description,
+            },
+        };
+
+        public override AnalyzerConfig ParseConfig(FileInfo file)
+        {
+            RuntimeHelpers.RunClassConstructor(typeof(NinoxConnivensConfig).TypeHandle);
+            var config = ConfigFile.Deserialize<NinoxConnivensConfig>(file);
+
+            // validation of configs can be done here
+            GenericRecognizer.ValidateProfileTagsMatchAlgorithms(config.Profiles, file);
+            return config;
+        }
+
+        public override RecognizerResults Recognize(
+            AudioRecording audioRecording,
+            Config configuration,
+            TimeSpan segmentStartOffset,
+            Lazy<IndexCalculateResult[]> getSpectralIndexes,
+            DirectoryInfo outputDirectory,
+            int? imageWidth)
+        {
+            var genericConfig = (NinoxConnivensConfig)configuration;
+            var recognizer = new GenericRecognizer();
+
+            // Use the generic recognizers to find all generic events.
+            RecognizerResults combinedResults = recognizer.Recognize(
+                audioRecording,
+                genericConfig,
+                segmentStartOffset,
+                getSpectralIndexes,
+                outputDirectory,
+                imageWidth);
+
+            return combinedResults;
+        }
+
+        public class NinoxConnivensConfig : GenericRecognizer.GenericRecognizerConfig
+        {
+        }
+    }
+}

src/AnalysisPrograms/Recognizers/Birds/NinoxStrenua.cs

@@ -26,7 +26,7 @@ namespace AnalysisPrograms.Recognizers
     /// Its conservation status is "threatened".
     /// This recognizer has been trained on good quality calls provided by NSW DPI by Brad Law and Kristen Thompson.
     /// </summary>
-    internal class NinoxStrenua : RecognizerBase
+    public class NinoxStrenua : RecognizerBase
     {
         private static readonly ILog PowerfulOwlLog = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
 
@@ -36,13 +36,15 @@ internal class NinoxStrenua : RecognizerBase
 
         public override string Description => "[ALPHA] Detects acoustic events for the Australian Powerful Owl.";
 
+        public override string CommonName => "Powerful Owl";
+
         public override AnalyzerConfig ParseConfig(FileInfo file)
         {
             RuntimeHelpers.RunClassConstructor(typeof(NinoxStrenuaConfig).TypeHandle);
             var config = ConfigFile.Deserialize<NinoxStrenuaConfig>(file);
 
             // validation of configs can be done here
-            GenericRecognizer.ValidateProfileTagsMatchAlgorithms(config.Profiles, file);
+            ValidateProfileTagsMatchAlgorithms(config.Profiles, file);
             return config;
         }