Fixes bug in multi recogniser (#496)

* Fixes bug in multi recogniser

The multirecogniser was not outputting any events after the component recognizers detected events.  The fix was simply to ensure NewEvents were aggregated as well as old style AcousticEvents.

Also:
- wrote tests for the multi recognizers
- ensured that multiple different ways of specifying sub-recognizers would work (name, soft-resolved config, absolute reference to files)
- also ensured configs were loaded before the main analysis starts - this should produce much nicer error messages and avoid cutting audio before telling the user about the inevitable failure.
- fixed the path to analysis programs in the test metdadata helper

Fixes #97

* Added some validation to MultiRecogniser AnalysisNames array

* Reverts change to MultiRecognizerConfig base class

It acts like a Recognizer and thus must be of type RecognizerConfig.

My attempt to generalize the concept in 9c95fa5 was misguided

src/AP.VersionBuild.targets

@@ -5,7 +5,7 @@
   <!-- Register our task that as something to run before standard build target -->
   <Target Name="APVersionBeforeBuild" BeforeTargets="PrepareForBuild">
     <!-- <Message Text="[APVersionBeforeBuild] Debug: $(RuntimeIdentifier)" Importance="High" /> -->
-    <Exec Command="pwsh –NonInteractive -noprofile $(ProjectDir)../git_version.ps1 -configuration $(Configuration) -self_contained $(SelfContained) -runtime_identifier '$(RuntimeIdentifier)'" ConsoleToMSBuild="True" EchoOff="false" StandardOutputImportance="low">
+    <Exec Command="pwsh –NonInteractive -noprofile $(ProjectDir)../git_version.ps1 -configuration $(Configuration) -self_contained $(SelfContained) -runtime_identifier &quot;$(RuntimeIdentifier)&quot; -target_framework &quot;$(TargetFramework.ToLowerInvariant())&quot;" ConsoleToMSBuild="True" EchoOff="false" StandardOutputImportance="low">
       <Output TaskParameter="ConsoleOutput" ItemName="VersionMetadata" />
     </Exec>
     <!-- <Message Text="[APVersionBeforeBuild] %(VersionMetadata.Identity)" Importance="High" /> -->

src/Acoustics.Shared/ConfigFile/Config.cs

@@ -7,6 +7,7 @@ namespace Acoustics.Shared.ConfigFile
     using System;
     using System.Collections.Generic;
     using System.Globalization;
+    using System.IO;
     using Acoustics.Shared.Contracts;
 
     public class Config : IConfig
@@ -47,6 +48,8 @@ private enum MatchType
 
         public string ConfigPath { get; set; }
 
+        public string ConfigDirectory => Path.GetDirectoryName(this.ConfigPath);
+
         /// <summary>
         /// Gets or sets the generic object graph that mirrors the configuration.
         /// This object is ignored for JSON serialization in log dumping if

src/Acoustics.Shared/Extensions/ExtensionsString.cs

@@ -402,6 +402,16 @@ public static bool IsNotWhitespace(this string str)
             return !string.IsNullOrWhiteSpace(str);
         }
 
+        public static string StripEnd(this string str, string suffix, StringComparison comparison = default)
+        {
+            if (suffix != null && str.EndsWith(suffix, comparison))
+            {
+                return str.Substring(0, str.Length - suffix.Length);
+            }
+
+            return str;
+        }
+
         public static string NormalizeToCrLf(this string str)
         {
             string normalized = Regex.Replace(str, @"\r\n|\n\r|\n|\r", "\r\n");

src/Acoustics.Shared/Extensions/FileInfoExtensions.cs

@@ -187,6 +187,13 @@ public static T RefreshInfo<T>(this T info)
             return info;
         }
 
+        public static FileInfo CopyTo(this FileInfo source, DirectoryInfo dest)
+        {
+            var result = Path.Combine(dest.FullName, source.Name);
+            source.CopyTo(result);
+            return result.ToFileInfo();
+        }
+
         public static string BaseName(this FileInfo file)
         {
             return Path.GetFileNameWithoutExtension(file.Name);

src/AnalysisBase/AnalyzerConfig.cs

@@ -15,7 +15,7 @@ public class AnalyzerConfig
         [Obsolete("The AnalysisName property is no longer used")]
         public string AnalysisName { get; set; }
 
-        public double EventThreshold { get; set; } = EventThresholdDefault;
+        public virtual double EventThreshold { get; set; } = EventThresholdDefault;
 
         /// <summary>
         /// Gets or sets the length of audio block to process.

src/AnalysisConfigFiles/.vscode/settings.json

@@ -2,5 +2,6 @@
     "cSpell.words": [
         "Nyquist",
         "Resample"
-    ]
+    ],
+    "python.pythonPath": "C:\\Python37\\python.exe"
 }

src/AnalysisConfigFiles/RecognizerConfigFiles/Ecosounds.MultiRecognizer.yml → src/AnalysisConfigFiles/RecognizerConfigFiles/QUT.MultiRecognizer.yml

@@ -8,7 +8,7 @@
 # LIST OF REQUIRED SPECIES RECOGNISERS
 # The items in this list need to match the value for `AnalysisName` in each of the individual species config files.
 # Note also, that the config file paths are resolved by appending '.yml' to the end of each item in the species list.
-SpeciesList:
+AnalysisNames:
 #  - Towsey.CriniaRemota
   - Towsey.LimnodynastesConvex
 #  - Towsey.LitoriaBicolor
@@ -24,9 +24,6 @@ SpeciesList:
 #  - Towsey.UperoleiaInundata
 #  - Towsey.UperoleiaLithomoda
 
-# Standard settings
-EventThreshold: 0.2
-
 
 ## Specifically for AnalyzeLongRecording
 # SegmentDuration: units=seconds;
@@ -35,7 +32,7 @@ SegmentDuration: 60
 SegmentOverlap: 0
 # Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 SaveIntermediateWavFiles: Never
-# If `true` saves a data into a seperate file every `SegmentDuration` seconds. Accepts a boolean value: [false|true]
+# If `true` saves a data into a separate file every `SegmentDuration` seconds. Accepts a boolean value: [false|true]
 SaveIntermediateCsvFiles: false
 # Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 SaveSonogramImages: True

src/AnalysisPrograms/AnalyseLongRecordings/AnalyseLongRecording.cs

@@ -119,7 +119,7 @@ public static void Execute(Arguments arguments)
 
             bool filenameDate = configuration.RequireDateInFilename;
 
-            if (configuration[AnalysisKeys.AnalysisName].IsNotWhitespace())
+            if (configuration.AnalysisName.IsNotWhitespace())
             {
                 Log.Warn("Your config file has `AnalysisName` set - this property is deprecated and ignored");
             }

src/AnalysisPrograms/Recognizers/Base/MultiRecognizer.cs

@@ -27,6 +27,7 @@ namespace AnalysisPrograms.Recognizers.Base
     using AnalysisPrograms.AnalyseLongRecordings;
     using AudioAnalysisTools;
     using AudioAnalysisTools.DSP;
+    using AudioAnalysisTools.Events;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.StandardSpectrograms;
     using AudioAnalysisTools.WavTools;
@@ -39,26 +40,22 @@ namespace AnalysisPrograms.Recognizers.Base
 
     public class MultiRecognizer : RecognizerBase
     {
-        public class MultiRecognizerConfig : RecognizerConfig
-        {
-            public string[] SpeciesList { get; set; }
-        }
+        private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
 
         public override string Description => "[BETA] A method to run multiple event/species recognisers, depending on entries in config file.";
 
-        public override string Author => "Ecosounds";
+        public override string Author => "QUT";
 
         public override string SpeciesName => "MultiRecognizer";
 
         public override string CommonName => string.Empty;
 
         public override Status Status => Status.Unmaintained;
 
-        private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
-
         public override AnalyzerConfig ParseConfig(FileInfo file)
         {
-            return ConfigFile.Deserialize<MultiRecognizerConfig>(file);
+            var config = ConfigFile.Deserialize<MultiRecognizerConfig>(file);
+            return config;
         }
 
         public override RecognizerResults Recognize(AudioRecording audioRecording, Config configuration, TimeSpan segmentStartOffset, Lazy<IndexCalculateResult[]> getSpectralIndexes, DirectoryInfo outputDirectory, int? imageWidth)
@@ -79,24 +76,17 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
             var scoreTracks = new List<Image<Rgb24>>();
             var plots = new List<Plot>();
             var events = new List<AcousticEvent>();
+            var newEvents = new List<EventCommon>();
 
             // Get list of ID names from config file
             // Loop through recognizers and accumulate the output
-            foreach (string name in multiRecognizerConfig.SpeciesList)
+            foreach (var pair in multiRecognizerConfig.Analyses)
             {
-                // AT: Fixed this... the following should not be needed. If it happens, let me know.
-                // SEEM TO HAVE LOST SAMPLES
-                //if (audioRecording.WavReader.Samples == null)
-                //{
-                //    Log.Error("audioRecording's samples are null - an inefficient disk operation is now needed");
-                //    audioRecording = new AudioRecording(audioRecording.FilePath);
-                //}
-
-                var output = DoCallRecognition(name, segmentStartOffset, audioRecording, getSpectralIndexes, outputDirectory, imageWidth.Value);
+                var output = DoCallRecognition(pair.Recognizer, pair.Configuration, segmentStartOffset, audioRecording, getSpectralIndexes, outputDirectory, imageWidth);
 
                 if (output == null)
                 {
-                    Log.Warn($"Recognizer for {name} returned a null output");
+                    Log.Warn($"Recognizer for {pair.Recognizer.DisplayName} returned a null output");
                 }
                 else
                 {
@@ -111,6 +101,8 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
                         events.AddRange(output.Events);
                     }
 
+                    newEvents.AddRange(output.NewEvents);
+
                     // rescale scale of plots
                     output.Plots.ForEach(p => p.ScaleDataArray(sonogram.FrameCount));
 
@@ -123,6 +115,7 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
             return new RecognizerResults()
             {
                 Events = events,
+                NewEvents = newEvents,
                 ScoreTrack = scoreTrackImage,
                 Sonogram = sonogram,
                 Plots = plots,
@@ -141,17 +134,8 @@ public override void SummariseResults(
             // no-op
         }
 
-        public static RecognizerResults DoCallRecognition(string name, TimeSpan segmentStartOffset, AudioRecording recording, Lazy<IndexCalculateResult[]> indices, DirectoryInfo outputDirectory, int imageWidth)
+        private static RecognizerResults DoCallRecognition(IEventRecognizer recognizer, RecognizerConfig configuration, TimeSpan segmentStartOffset, AudioRecording recording, Lazy<IndexCalculateResult[]> indices, DirectoryInfo outputDirectory, int? imageWidth)
         {
-            Log.Debug("Looking for recognizer and config files for " + name);
-
-            // find an appropriate event recognizer
-            var recognizer = AnalyseLongRecording.FindAndCheckAnalyzer<IEventRecognizer>(name, name + ".yml");
-
-            // load up the standard config file for this species
-            var configurationFile = ConfigFile.Resolve(name + ".yml");
-            var configuration = recognizer.ParseConfig(configurationFile);
-
             // TODO: adapt sample rate to required rate
             int? resampleRate = configuration.ResampleRate;
             if (resampleRate.HasValue && recording.WavReader.SampleRate != resampleRate.Value)
@@ -160,17 +144,17 @@ public static RecognizerResults DoCallRecognition(string name, TimeSpan segmentS
             }
 
             // execute it
-            Log.Info("MultiRecognizer: Executing single recognizer " + name);
+            Log.Info("MultiRecognizer: Executing single recognizer " + recognizer.DisplayName);
             RecognizerResults result = recognizer.Recognize(
                 recording,
                 configuration,
                 segmentStartOffset,
                 indices,
                 outputDirectory,
                 imageWidth);
-            Log.Debug("MultiRecognizer: Completed single recognizer" + name);
+            Log.Debug("MultiRecognizer: Completed single recognizer" + recognizer.DisplayName);
 
-            var scoreTracks = result.Plots.Select(p => GenerateScoreTrackImage(name, p?.data, imageWidth)).ToList();
+            var scoreTracks = result.Plots.Select(p => GenerateScoreTrackImage(recognizer.DisplayName, p?.data, imageWidth ?? result.Sonogram.FrameCount)).ToList();
             if (scoreTracks.Count != 0)
             {
                 result.ScoreTrack = ImageTools.CombineImagesVertically(scoreTracks);
@@ -179,7 +163,7 @@ public static RecognizerResults DoCallRecognition(string name, TimeSpan segmentS
             return result;
         }
 
-        public static Image<Rgb24> GenerateScoreTrackImage(string name, double[] scores, int imageWidth)
+        private static Image<Rgb24> GenerateScoreTrackImage(string name, double[] scores, int imageWidth)
         {
             Log.Info("MultiRecognizer.GenerateScoreTrackImage(): " + name);
             if (scores == null)
@@ -223,5 +207,55 @@ public static Image<Rgb24> GenerateScoreTrackImage(string name, double[] scores,
             });
             return trackImage;
         }
+
+        public class MultiRecognizerConfig : RecognizerConfig
+        {
+            public MultiRecognizerConfig()
+            {
+                void OnLoaded(IConfig eventConfig)
+                {
+                    MultiRecognizerConfig config = (MultiRecognizerConfig)eventConfig;
+
+                    if (config.AnalysisNames is null or { Length: 0 })
+                    {
+                        throw new ConfigFileException(
+                            $"{ nameof(this.AnalysisNames)} cannot be null or empty. It should be a list with at least one config file in it.",
+                            config.ConfigPath);
+                    }
+
+                    // load the other config files
+                    this.Analyses =
+                        config
+                        .AnalysisNames
+                        .Select(x => x.EndsWith(".yml") ? x : x + ".yml")
+                        .Select(lookup =>
+                        {
+                            Log.Debug("Looking for config files for " + lookup);
+                            var configurationFile = ConfigFile.Resolve(lookup, config.ConfigDirectory.ToDirectoryInfo());
+
+                            // find an appropriate event recognizer
+                            var recognizer = AnalyseLongRecording.FindAndCheckAnalyzer<IEventRecognizer>(null, configurationFile.Name);
+
+                            // load up the standard config file for this species
+                            var configuration = (RecognizerConfig)recognizer.ParseConfig(configurationFile);
+
+                            return (recognizer, configuration);
+                        }).ToArray();
+                }
+
+                this.Loaded += OnLoaded;
+            }
+
+            public string[] AnalysisNames { get; set; }
+
+            /// <summary>
+            /// Gets or sets the threshold for which to filter events.
+            /// Defaults to 0.0 for the multi recogniser as we want the base recogniser's filters to be used.
+            /// </summary>
+            public override double EventThreshold { get; set; } = 0.0;
+
+            internal (IEventRecognizer Recognizer, RecognizerConfig Configuration)[] Analyses { get; set; }
+        }
     }
+
 }

src/AssemblyMetadata.cs.template

@@ -44,6 +44,7 @@ namespace AnalysisPrograms
         public const bool CompiledAsSelfContained = ${self_contained};
         public const string CompiledRuntimeIdentifer = "${runtime_identifier}";
         public const string CompiledConfiguration = "${configuration}";
+        public const string CompiledTargetFramework = "${target_framework}";
 
         public static readonly Version Version = new Version("${version}");
     }

src/git_version.ps1

@@ -5,6 +5,7 @@ param(
     [string]$configuration,
     [string]$self_contained,
     [string]$runtime_identifier,
+    [string]$target_framework,
     [switch]$set_ci = $false,
     [switch]$json = $false,
     [switch]$env_vars = $false,
@@ -144,7 +145,7 @@ elseif ($json) {
 }
 elseif ($env_vars) {
     # https://github.com/PowerShell/PowerShell/issues/5543
-    # Due to a bug with set-content, it cna't bind to the property for a value in
+    # Due to a bug with set-content, it can't bind to the property for a value in
     # an object, which makes the pipeline version rather intolerable.
     # Hence we're adding a toString() to our pscustomobject that ensures only
     # the value is represented when Set-Content calls toString