Merge branch 'master' of https://github.com/QutBioacoustics/audio-ana…

…lysis

Original hash: 5824951

Acoustics/Acoustics.Shared/Acoustics.Shared.csproj

@@ -86,6 +86,7 @@
     <CodeContractsSuggestAssumptionsForCallees>False</CodeContractsSuggestAssumptionsForCallees>
     <CodeContractsNecessaryEnsures>True</CodeContractsNecessaryEnsures>
     <CodeContractsSkipAnalysisIfCannotConnectToCache>False</CodeContractsSkipAnalysisIfCannotConnectToCache>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
     <DebugType>pdbonly</DebugType>
@@ -138,6 +139,7 @@
     <CodeContractsEmitXMLDocs>False</CodeContractsEmitXMLDocs>
     <CodeContractsCacheAnalysisResults>True</CodeContractsCacheAnalysisResults>
     <CodeContractsSkipAnalysisIfCannotConnectToCache>False</CodeContractsSkipAnalysisIfCannotConnectToCache>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <ItemGroup>
     <Reference Include="CsvHelper, Version=2.0.0.0, Culture=neutral, PublicKeyToken=8c4959082be5c823, processorArchitecture=MSIL">
@@ -229,6 +231,7 @@
     <Compile Include="Range.cs" />
     <Compile Include="ResultProperty.cs" />
     <Compile Include="SegmentPolicy.cs" />
+    <Compile Include="Span.cs" />
     <Compile Include="SqlServerTypes\Loader.cs" />
     <Compile Include="StatDescriptive.cs" />
     <Compile Include="StringKeyValueStore.cs" />

Acoustics/Acoustics.Shared/AppConfigHelper.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="AppConfigHelper.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the AppConfigHelper type.

Acoustics/Acoustics.Shared/ConfigFile/ConfigFile.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ConfigFile.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the ConfigFile type.

Acoustics/Acoustics.Shared/ConfigFile/ConfigFileException.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ConfigFileException.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the ConfigFileException type.

Acoustics/Acoustics.Shared/Csv/Csv.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="Csv.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Generic methods for reading and writing Csv file.

Acoustics/Acoustics.Shared/Csv/CsvExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="AnalysisProgramsClassMapper.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the AnalysisProgramsClassMapper type.

Acoustics/Acoustics.Shared/Csv/ISetPointConverter.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="SetPointConverter.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the ISetPointConverter type.

Acoustics/Acoustics.Shared/Csv/MatrixMapper.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="MatrixMapper.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the TwoDimensionalArray type.

Acoustics/Acoustics.Shared/Debugging/AutoAttachVs.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="AutoAttachVs.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Example taken from this gist.

Acoustics/Acoustics.Shared/Extensions/ArrayExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ArrayExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the ArrayExtensions type.

Acoustics/Acoustics.Shared/Extensions/DateTimeAndTimeSpanExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ExtensionsDateTime.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   
@@ -303,5 +303,25 @@ public static TimeSpan Multiply(this TimeSpan multiplicand, double multiplier)
         {
             return TimeSpan.FromTicks((long)(multiplicand.Ticks * multiplier));
         }
+
+        // https://github.com/exceptionless/Exceptionless.DateTimeExtensions/blob/master/src/Exceptionless.DateTimeExtensions/DateTimeOffsetExtensions.cs#L222
+        public static DateTimeOffset Floor(this DateTimeOffset date, TimeSpan interval)
+        {
+            return date.AddTicks(-(date.Ticks % interval.Ticks));
+        }
+
+        // https://github.com/exceptionless/Exceptionless.DateTimeExtensions/blob/master/src/Exceptionless.DateTimeExtensions/DateTimeOffsetExtensions.cs#L226
+        public static DateTimeOffset Ceiling(this DateTimeOffset date, TimeSpan interval)
+        {
+            return date.AddTicks(interval.Ticks - (date.Ticks % interval.Ticks));
+        }
+
+        // https://github.com/exceptionless/Exceptionless.DateTimeExtensions/blob/master/src/Exceptionless.DateTimeExtensions/DateTimeOffsetExtensions.cs#L230
+        public static DateTimeOffset Round(this DateTimeOffset date, TimeSpan roundingInterval)
+        {
+            var halfIntervalTicks = ((roundingInterval.Ticks + 1) >> 1);
+            return date.AddTicks(halfIntervalTicks - ((date.Ticks + halfIntervalTicks) % roundingInterval.Ticks));
+        }
+
     }
 }

Acoustics/Acoustics.Shared/Extensions/DoubleExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="DoubleExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the DoubleExtensions type.

Acoustics/Acoustics.Shared/Extensions/DoubleSquareArrayExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="DoubleSquareArrayExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   

Acoustics/Acoustics.Shared/Extensions/EnumerableExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="EnumerableExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 // --------------------------------------------------------------------------------------------------------------------
 

Acoustics/Acoustics.Shared/Extensions/FileInfoExtensions.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="FileInfoExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the FileInfoExtensions type.

Acoustics/Acoustics.Shared/Extensions/ReflectionExtensions.cs

@@ -1,7 +1,7 @@
 // ReSharper disable once CheckNamespace
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ReflectionExtensions.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the ReflectionExtensions type.

Acoustics/Acoustics.Shared/FileDateHelpers.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="FileDateHelpers.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the FileDateHelpers type.
@@ -23,6 +23,15 @@ namespace Acoustics.Shared
 
     public class FileDateHelpers
     {
+        private static readonly string[] AcceptedFormatsNoTimeZone = {
+                "yyyyMMdd[-|T|_]HHmmss (if timezone offset hint provided)",
+                "yyyyMMdd[-|T|_]HHmmssZ"
+            };
+
+        private static readonly string[] AcceptedFormatsTimeZone = {
+                "yyyyMMdd[-|T|_]HHmmss[+|-]HH",
+                "yyyyMMdd[-|T|_]HHmmss[+|-]HHmm"
+            };
 
         internal static readonly DateVariants[] PossibleFormats =
             {
@@ -32,7 +41,8 @@ public class FileDateHelpers
                 new DateVariants(
                     @"^(.*)(?<date>(\d{4})(\d{2})(\d{2})(?<separator>T|-|_)(\d{2})(\d{2})(\d{2})(?![+-][\d:]{2,5}|Z)).*\.([a-zA-Z0-9]+)$",
                      AppConfigHelper.StandardDateFormatNoTimeZone, 
-                    false),
+                    false,
+                    AcceptedFormatsNoTimeZone),
 
                 // valid: prefix_20140101-235959+10.mp3, a_00000000-000000+00.a, a_99999999-999999+9999.dnsb48364JSFDSD                                    
                 // valid: prefix_20140101_235959+10.mp3, a_00000000_000000+00.a, a_99999999_999999+9999.dnsb48364JSFDSD                                    
@@ -41,7 +51,7 @@ public class FileDateHelpers
                 new DateVariants(
                     @"^(.*)(?<date>(\d{4})(\d{2})(\d{2})(?<separator>T|-|_)(\d{2})(\d{2})(\d{2})(?![+-][:]{2,5})(?<offset>([+-](?!\d{0,5}:)(\d{4}|\d{2}))|Z)).*\.([a-zA-Z0-9]+)",
                     AppConfigHelper.StandardDateFormat,
-                    true),
+                    true, AcceptedFormatsTimeZone),
             };
 
         private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
@@ -205,18 +215,21 @@ private static bool ParseFileDateTimeBase(
 
         internal class DateVariants
         {
-            public DateVariants(string regex, string parseFormat, bool parseTimeZone)
+            public DateVariants(string regex, string parseFormat, bool parseTimeZone, string[] acceptedFormats)
             {
                 this.Regex = regex;
                 this.ParseFormat = parseFormat;
                 this.ParseTimeZone = parseTimeZone;
+                this.AcceptedFormats = acceptedFormats;
             }
 
-            public string Regex { get; set; }
+            public string Regex { get; }
+
+            public string ParseFormat { get; }
 
-            public string ParseFormat { get; set; }
+            public bool ParseTimeZone{ get; }
 
-            public bool ParseTimeZone{ get; set; }
+            public string[] AcceptedFormats { get; }
 
         }
     }
@@ -229,17 +242,10 @@ public InvalidFileDateException(string message)
             : base(message)
         {
             this.options = "\n Valid formats include:  \n"
-                           + FileDateHelpers.PossibleFormats.Select(x => x.ParseFormat)
-                                 .Distinct()
+                           + FileDateHelpers.PossibleFormats.SelectMany(x => x.AcceptedFormats)
                                  .Aggregate(string.Empty, (s, x) => s += "\t - " + x + "\n");
         }
 
-        public override string Message
-        {
-            get
-            {
-                return base.Message + this.options;
-            }
-        }
+        public override string Message => base.Message + this.options;
     }
 }

Acoustics/Acoustics.Shared/Json.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="Json.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the Json type.

Acoustics/Acoustics.Shared/Span.cs

@@ -0,0 +1,40 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+
+namespace Acoustics.Shared
+{
+    public struct Span<T> : IEquatable<Span<T>>, IComparable<Span<T>> where T : struct, IComparable<T>
+    {
+        public Span(T lower, T upper)
+        {
+            this.Lower = lower;
+            this.Upper = upper;
+        }
+
+        public T Lower { get; }
+        public T Upper { get; }
+
+        public bool Equals(Span<T> other)
+        {
+            return this.Lower.Equals(other.Lower) && this.Upper.Equals(other.Upper);
+        }
+
+        public int CompareTo(Span<T> other)
+        {
+            var lower = this.Lower.CompareTo(other.Lower);
+            var upper = this.Upper.CompareTo(other.Upper);
+
+            return lower == 0 ? upper : lower;
+        }
+    }
+
+    public static class Span
+    {
+        public static Span<T> Create<T>(T minimum, T maximum) where T : struct, IComparable<T>
+        {
+            return new Span<T>(minimum, maximum);
+        }
+    }
+}

Acoustics/Acoustics.Shared/Yaml.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="Yaml.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Defines the Yaml type.

Acoustics/Acoustics.Shared/app.config

@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <configuration>
   <runtime>
     <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
       <dependentAssembly>
-        <assemblyIdentity name="YamlDotNet" publicKeyToken="2b53052c5884d7a1" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-2.0.1.21004" newVersion="2.0.1.21004" />
+        <assemblyIdentity name="YamlDotNet" publicKeyToken="2b53052c5884d7a1" culture="neutral"/>
+        <bindingRedirect oldVersion="0.0.0.0-2.0.1.21004" newVersion="2.0.1.21004"/>
       </dependentAssembly>
     </assemblyBinding>
   </runtime>
-</configuration>
+<startup><supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.0"/></startup></configuration>

Acoustics/Acoustics.Shared/packages.config

@@ -4,7 +4,7 @@
   <package id="fasterflect" version="2.1.3" targetFramework="net4" />
   <package id="log4net" version="2.0.3" targetFramework="net4" />
   <package id="Microsoft.SqlServer.Types" version="11.0.2" targetFramework="net4" />
-  <package id="Newtonsoft.Json" version="6.0.3" targetFramework="net4" />
+  <package id="Newtonsoft.Json" version="6.0.3" targetFramework="net40" />
   <package id="YamlDotNet" version="3.9.0" targetFramework="net40" />
   <package id="YamlDotNet.Dynamic" version="3.2.3" targetFramework="net40" />
 </packages>

Acoustics/Acoustics.Test/ArrayExtensionsTests.cs

@@ -1,6 +1,6 @@
 // --------------------------------------------------------------------------------------------------------------------
 // <copyright file="ArrayExtensionsTests.cs" company="QutBioacoustics">
-//   All code in this file and all associated files are the copyright of the QUT Bioacoustics Research Group (formally MQUTeR).
+//   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>
 //   Summary description for ArrayExtensionsTests