Finished Generic recognizer and tests

- refactored classes according to conventions and added various bits of documentation
- added support for YAML serialization and deserialization of type tags. This allows us to deserialize arrays/maps with variably typed elements.
- added an automatically generated YAML schema for the generic recognizer config
- added a full suite of tests for generic recognizer, including the re-use of algorithms in multiple profiles
- added a hand crafted audio test fixture that made it easy to write said tests

Note: the whistle component and associated test currently fail because @towsey has not completed that algorithm yet.

AudioAnalysis.sln.DotSettings

@@ -4,12 +4,16 @@
 	<s:Boolean x:Key="/Default/CodeInspection/Highlighting/ReadSettingsFromFileLevel/@EntryValue">True</s:Boolean>
 	<s:String x:Key="/Default/CodeStyle/CodeFormatting/CSharpCodeStyle/ThisQualifier/INSTANCE_MEMBERS_QUALIFY_MEMBERS/@EntryValue">15</s:String>
 	<s:Int64 x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/BLANK_LINES_BEFORE_SINGLE_LINE_COMMENT/@EntryValue">1</s:Int64>
+	<s:Int64 x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/MAX_ARRAY_INITIALIZER_ELEMENTS_ON_LINE/@EntryValue">1</s:Int64>
+	<s:Int64 x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/MAX_FORMAL_PARAMETERS_ON_LINE/@EntryValue">9999</s:Int64>
+	<s:Int64 x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/MAX_INITIALIZER_ELEMENTS_ON_LINE/@EntryValue">1</s:Int64>
 	<s:String x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/PLACE_ACCESSORHOLDER_ATTRIBUTE_ON_SAME_LINE_EX/@EntryValue">NEVER</s:String>
 	<s:Boolean x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/PLACE_SIMPLE_ACCESSORHOLDER_ON_SINGLE_LINE/@EntryValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/SPACE_AFTER_TYPECAST_PARENTHESES/@EntryValue">False</s:Boolean>
 	<s:Boolean x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/SPACE_WITHIN_SINGLE_LINE_ARRAY_INITIALIZER_BRACES/@EntryValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/CodeStyle/CodeFormatting/CSharpFormat/STICK_COMMENT/@EntryValue">False</s:Boolean>
 
+
 	<s:String x:Key="/Default/CodeStyle/CSharpFileLayoutPatterns/Pattern/@EntryValue">&lt;?xml version="1.0" encoding="utf-16"?&gt;&#xD;
 &lt;Patterns xmlns="urn:schemas-jetbrains-com:member-reordering-patterns"&gt;&#xD;
   &lt;TypePattern DisplayName="Non-reorderable types"&gt;&#xD;
@@ -188,6 +192,7 @@
 &lt;/Patterns&gt;</s:String>
 	<s:Boolean x:Key="/Default/CodeStyle/CSharpUsing/AddImportsToDeepestScope/@EntryValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/CodeStyle/CSharpUsing/QualifiedUsingAtNestedScope/@EntryValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/CodeStyle/EditorConfig/EnableStyleCopSupport/@EntryValue">True</s:Boolean>
 	<s:String x:Key="/Default/CodeStyle/Naming/CSharpNaming/PredefinedNamingRules/=PrivateInstanceFields/@EntryIndexedValue">&lt;Policy Inspect="True" Prefix="" Suffix="" Style="aaBb" /&gt;</s:String>
 	<s:String x:Key="/Default/CodeStyle/Naming/CSharpNaming/PredefinedNamingRules/=PrivateStaticFields/@EntryIndexedValue">&lt;Policy Inspect="True" Prefix="" Suffix="" Style="aaBb" /&gt;</s:String>
 	<s:String x:Key="/Default/CodeStyle/Naming/JavaScriptNaming/UserRules/=JS_005FBLOCK_005FSCOPE_005FCONSTANT/@EntryIndexedValue">&lt;Policy Inspect="True" Prefix="" Suffix="" Style="aaBb" /&gt;</s:String>
@@ -283,11 +288,14 @@
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Bioacoustics/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Chromeless/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=dedupe/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=DTMF/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Ecosounds/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=ffmpeg/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=ffprobe/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=flac/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Pteropus/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Redirector/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=resampled/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=spectrograms/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Submatrix/@EntryIndexedValue">True</s:Boolean>
   <s:Boolean x:Key="/Default/UserDictionary/Words/=Anthony/@EntryIndexedValue">True</s:Boolean>

src/Acoustics.Shared/Acoustics.Shared.csproj

@@ -208,7 +208,8 @@
     <Compile Include="ConfigFile\ConfigFile.Profiles.cs" />
     <Compile Include="ConfigFile\ConfigFileException.cs" />
     <Compile Include="ConfigFile\IConfig.cs" />
-    <Compile Include="ConfigFile\IProfile.cs" />
+    <Compile Include="ConfigFile\INamedProfiles.cs" />
+    <Compile Include="ConfigFile\IProfiles.cs" />
     <Compile Include="Contracts\Contract.cs" />
     <Compile Include="Csv\CsvExtensions.cs" />
     <Compile Include="Csv\Csv.cs" />

src/Acoustics.Shared/ConfigFile/INamedProfiles.cs

@@ -0,0 +1,21 @@
+// <copyright file="INamedProfiles.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 Acoustics.Shared.ConfigFile
+{
+    using System.Collections.Generic;
+
+    /// <summary>
+    /// Allows a <see cref="Config"/> class to have profiles.
+    /// </summary>
+    /// <typeparam name="T">The type of each expected profile.</typeparam>
+    public interface INamedProfiles<T>
+    {
+        /// <summary>
+        /// Gets a collection of named profiles that allow for
+        /// variable and configurable algorithms to be used.
+        /// </summary>
+        Dictionary<string, T> Profiles { get; }
+    }
+}

src/Acoustics.Shared/ConfigFile/IProfiles.cs

@@ -0,0 +1,21 @@
+// <copyright file="IProfiles.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 Acoustics.Shared.ConfigFile
+{
+    using System.Collections.Generic;
+
+    /// <summary>
+    /// Allows a <see cref="Config"/> class to have profiles.
+    /// </summary>
+    /// <typeparam name="T">The type of each expected profile.</typeparam>
+    public interface IProfiles<out T>
+    {
+        /// <summary>
+        /// Gets a collection of unnamed profiles that allow for
+        /// variable and configurable algorithms to be used.
+        /// </summary>
+        IReadOnlyCollection<T> Profiles { get; }
+    }
+}

src/Acoustics.Shared/Extensions/FileInfoExtensions.cs

@@ -17,6 +17,7 @@ namespace System
     using System;
     using Text;
     using Acoustics.Shared.Contracts;
+    using JetBrains.Annotations;
     using log4net;
 
     public static class FileInfoExtensions
@@ -177,6 +178,8 @@ public static string FormatList(this IEnumerable<FileSystemInfo> infos)
         {
             return infos.Select(x => x.FullName).FormatList();
         }
+
+        public static string[] ReadAllLines([NotNull] this FileInfo file) => File.ReadAllLines(file.FullName);
     }
 
     public class FileInfoNameComparer : IComparer<FileInfo>, IEqualityComparer<FileInfo>

src/Acoustics.Shared/Yaml.cs

@@ -10,17 +10,47 @@
 namespace Acoustics.Shared
 {
     using System;
+    using System.Collections.Generic;
     using System.IO;
+    using System.Linq;
+    using JetBrains.Annotations;
     using YamlDotNet.Core;
-    using YamlDotNet.Core.Events;
-    using YamlDotNet.RepresentationModel;
     using YamlDotNet.Serialization;
 
     using Zio;
 
-    public class Yaml
+    public static class Yaml
     {
-        internal static IDeserializer Deserializer => new DeserializerBuilder().IgnoreUnmatchedProperties().Build();
+        private static readonly Dictionary<string, Type> TagMappings = new Dictionary<string, Type>();
+
+        internal static IDeserializer Deserializer => new DeserializerBuilder()
+            .IgnoreUnmatchedProperties()
+            .WithTagMappings(TagMappings)
+            .Build();
+
+        /// <summary>
+        /// Registers a type and a tag name that will be emitted in a YAML document when
+        /// serializing, and will allow for unambiguous parsing when deserializing.
+        /// </summary>
+        /// <typeparam name="T">The type to register.</typeparam>
+        /// <param name="name">The tag name to use.</param>
+        public static void AddTagMapping<T>(string name = null)
+        {
+            // yml type tags must be prefixed with an "!" character.
+            if (name == null)
+            {
+                name = "!" + typeof(T).Name;
+            }
+            else
+            {
+                if (name[0] != '!')
+                {
+                    name = "!" + name;
+                }
+            }
+
+            TagMappings.Add(name, typeof(T));
+        }
 
         public static T Deserialize<T>(FileInfo file)
         {
@@ -44,11 +74,14 @@ public static T Deserialize<T>(TextReader stream)
             return deserializer.Deserialize<T>(parser);
         }
 
-        public static void Serialize<T>(FileInfo file, T obj)
+        public static void Serialize<T>([NotNull] FileInfo file, [CanBeNull] T obj)
         {
             using (var stream = file.CreateText())
             {
-                var serializer = new SerializerBuilder().EmitDefaults().Build();
+                var serializer = new SerializerBuilder()
+                    .EmitDefaults()
+                    .WithTagMappings(TagMappings)
+                    .Build();
 
                 serializer.Serialize(stream, obj);
             }
@@ -73,5 +106,18 @@ internal static (object, T) LoadAndDeserialize<T>(string path)
                 return (generic, obj);
             }
         }
+
+        /// <summary>
+        /// A helper extension method that registers multiple tag mappings with
+        /// the <see cref="SerializerBuilder"/> or the <see cref="DeserializerBuilder"/>.
+        /// </summary>
+        private static T WithTagMappings<T>(
+            this T builder,
+            Dictionary<string, Type> mappings)
+            where T : BuilderSkeleton<T>
+        {
+            return mappings
+                .Aggregate(builder, (b, kvp) => b.WithTagMapping(kvp.Key, kvp.Value));
+        }
     }
 }

src/AnalysisConfigFiles/RecognizerConfigFiles/Ecosounds.GenericRecognizers.schema.yml

@@ -0,0 +1,65 @@
+Profiles:
+  TestAed: !AedParameters
+    IntensityThreshold: 0
+    SmallAreaThreshold: 0
+    BandpassMinimum: 
+    BandpassMaximum: 
+    NoiseReductionType: None
+    BgNoiseThreshold: 0
+    ResampleRate: 0
+    IncludeHitElementsInOutput: false
+    ConfigPath: 
+    GenericConfig: 
+  TestOscillation: !OscillationParameters
+    DctDuration: 1
+    DctThreshold: 0.5
+    MinOscillationFrequency: 6
+    MaxOscillationFrequency: 4
+    EventThreshold: 0.29999999999999999
+    ComponentName: 
+    SpeciesName: 
+    FrameSize: 
+    FrameStep: 
+    BgNoiseThreshold: 
+    MinHertz: 0
+    MaxHertz: 0
+    BottomHertzBuffer: 0
+    TopHertzBuffer: 
+    MinDuration: 1
+    MaxDuration: 10
+    DecibelThreshold: 6
+  TestBlob: !BlobParameters
+    ComponentName: 
+    SpeciesName: 
+    FrameSize: 
+    FrameStep: 
+    BgNoiseThreshold: 
+    MinHertz: 800
+    MaxHertz: 8000
+    BottomHertzBuffer: 0
+    TopHertzBuffer: 
+    MinDuration: 1
+    MaxDuration: 10
+    DecibelThreshold: 6
+  TestWhistle: !WhistleParameters
+    ComponentName: 
+    SpeciesName: 
+    FrameSize: 
+    FrameStep: 
+    BgNoiseThreshold: 
+    MinHertz: 0
+    MaxHertz: 0
+    BottomHertzBuffer: 0
+    TopHertzBuffer: 
+    MinDuration: 1
+    MaxDuration: 10
+    DecibelThreshold: 6
+HighResolutionIndicesConfig: 
+EventThreshold: 0.2
+SegmentDuration: 60
+SegmentOverlap: 0
+ResampleRate: 22050
+SaveIntermediateWavFiles: False
+SaveIntermediateCsvFiles: false
+SaveSonogramImages: False
+RequireDateInFilename: false