Adds unit tests for ribbon plots

src/Acoustics.Shared/Extensions/DateTimeAndTimeSpanExtensions.cs

@@ -11,6 +11,7 @@
 namespace System
 {
     using System.IO;
+    using Acoustics.Shared;
     using Collections.Generic;
     using Linq;
 
@@ -126,6 +127,19 @@ public static string ToTimeZoneString(this TimeSpan ts)
             return (ts < TimeSpan.Zero ? "-" : string.Empty) + ts.ToString(@"mm\:ss");
         }
 
+        /// <summary>
+        /// Formats a date in an ISO8601 format that is compact
+        /// and does not contain colons.
+        /// </summary>
+        /// <param name="date">The date to convert to a string.</param>
+        /// <returns>The resulting string.</returns>
+        public static string ToIso8601SafeString(this DateTimeOffset date)
+        {
+            return date
+                .ToString(AppConfigHelper.Iso8601FileCompatibleDateFormat)
+                .Replace(":", string.Empty);
+        }
+
         /// <summary>
         /// Gets the DateTimeOffset formatted as a javascript timestamp.
         /// </summary>
@@ -421,8 +435,6 @@ public static TimeSpan Max(this TimeSpan t1, TimeSpan t2)
             return t1 >= t2 ? t1 : t2;
         }
 
-
-
         public enum RoundingDirection
         {
             Floor,

src/Acoustics.Shared/Extensions/ExtensionsString.cs

@@ -1,4 +1,4 @@
-// -----------------------------------------------------------------------
+// -----------------------------------------------------------------------
 // <copyright file="ExtensionsString.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>
@@ -404,5 +404,16 @@ public static string NormalizeToCrLf(this string str)
             string normalized = Regex.Replace(str, @"\r\n|\n\r|\n|\r", "\r\n");
             return normalized;
         }
+
+        public static string FormatList(this IEnumerable<string> strings)
+        {
+            var builder = new StringBuilder("\n", 1000);
+            foreach (var value in strings)
+            {
+                builder.AppendFormat("\t- {0}\n", value);
+            }
+
+            return builder.ToString();
+        }
     }
 }

src/Acoustics.Shared/Extensions/FileInfoExtensions.cs

@@ -175,13 +175,7 @@ public static string BaseName(this FileInfo file)
 
         public static string FormatList(this IEnumerable<FileSystemInfo> infos)
         {
-            var builder = new StringBuilder("\n", 1000);
-            foreach (var info in infos)
-            {
-                builder.AppendFormat("\t- {0}\n", info.FullName);
-            }
-
-            return builder.ToString();
+            return infos.Select(x => x.FullName).FormatList();
         }
     }
 

src/Acoustics.Shared/FileNameHelpers.cs

@@ -1,4 +1,4 @@
-// <copyright file="FileNameHelpers.cs" company="QutEcoacoustics">
+// <copyright file="FileNameHelpers.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>
 
@@ -79,7 +79,18 @@ public static string AnalysisResultName(string baseName, string analysisTag, str
 
             if (otherSegments.Length > 0)
             {
-                filename += otherSegments.Aggregate(string.Empty, (aggregate, item) => aggregate + SegmentSeparator + item);
+                string result = string.Empty;
+                foreach (var segment in otherSegments)
+                {
+                    if (segment.IsNullOrEmpty())
+                    {
+                        continue;;
+                    }
+
+                    result = result + SegmentSeparator + segment;
+                }
+
+                filename += result;
             }
 
             if (!string.IsNullOrWhiteSpace(newExtension))

src/AnalysisPrograms/AcousticIndices.cs

@@ -275,7 +275,7 @@ public void SummariseResults(AnalysisSettings settings, FileSegment inputFileSeg
 
             string basename = Path.GetFileNameWithoutExtension(sourceAudio.Name);
 
-            // output to disk (so other analysers can use the data,
+            // output to disk (so other analyzers can use the data,
             // only data - configuration settings that generated these indices
             // this data can then be used by post-process analyses
             /* NOTE: The value for FrameStep is used only when calculating a standard spectrogram

src/AnalysisPrograms/AnalysisPrograms.csproj

@@ -375,8 +375,8 @@
     <Compile Include="Recognizers\LitoriaOlong.cs" />
     <Compile Include="Recognizers\LitoriaFallax.cs" />
     <Compile Include="Recognizers\RhinellaMarina.cs" />
-    <Compile Include="RibbonPlots\RibbonPlot.Arguments.cs" />
-    <Compile Include="RibbonPlots\RibbonPlot.Entry.cs" />
+    <Compile Include="Draw\RibbonPlots\RibbonPlot.Arguments.cs" />
+    <Compile Include="Draw\RibbonPlots\RibbonPlot.Entry.cs" />
     <Compile Include="SourcePreparers\RemoteSourcePreparer.cs" />
     <Compile Include="SourcePreparers\LocalSourcePreparer.cs" />
     <Compile Include="SourcePreparers\RemoteSourcePreparerException.cs" />

src/AnalysisPrograms/RibbonPlots/RibbonPlot.Arguments.cs → src/AnalysisPrograms/Draw/RibbonPlots/RibbonPlot.Arguments.cs

@@ -2,7 +2,7 @@
 // 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.RibbonPlots
+namespace AnalysisPrograms.Draw.RibbonPlots
 {
     using System;
     using System.IO;
@@ -27,8 +27,8 @@ public class Arguments : SubCommandBase
         {
             [Argument(
                 0,
-                Description = "One or more directories where that contain ribbon FCS files.")]
-            public DirectoryInfo[] SourceDirectories { get; set; }
+                Description = "One or more directories where that contain ribbon FCS files (index results).")]
+            public DirectoryInfo[] InputDirectories { get; set; }
 
             [Option(
                 CommandOptionType.SingleValue,
@@ -52,7 +52,7 @@ public class Arguments : SubCommandBase
 
             public override Task<int> Execute(CommandLineApplication app)
             {
-                return RibbonPlot.Execute(this);
+                return Draw.RibbonPlots.RibbonPlot.Execute(this);
             }
         }
     }

src/AnalysisPrograms/RibbonPlots/RibbonPlot.Entry.cs → src/AnalysisPrograms/Draw/RibbonPlots/RibbonPlot.Entry.cs

@@ -2,26 +2,22 @@
 // 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.RibbonPlots
+namespace AnalysisPrograms.Draw.RibbonPlots
 {
     using System;
     using System.Collections.Generic;
     using System.IO;
     using System.Linq;
-    using System.Security.Cryptography;
-    using System.Text;
     using System.Threading.Tasks;
     using Acoustics.Shared;
     using AnalysisPrograms.Production;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.LongDurationSpectrograms;
     using log4net;
-    using log4net.Util;
     using SixLabors.Fonts;
     using SixLabors.ImageSharp;
     using SixLabors.ImageSharp.PixelFormats;
     using SixLabors.ImageSharp.Processing;
-    using SixLabors.ImageSharp.Processing.Processors;
     using SixLabors.Primitives;
     using SixLabors.Shapes;
 
@@ -33,24 +29,24 @@ public partial class RibbonPlot
         private static readonly TimeSpan RibbonPlotDomain = TimeSpan.FromHours(24);
         private static readonly ILog Log = LogManager.GetLogger(nameof(RibbonPlot));
 
-        public static async Task<int> Execute(Arguments arguments)
+        public static async Task<int> Execute(RibbonPlot.Arguments arguments)
         {
-            if (arguments.SourceDirectories.IsNullOrEmpty())
+            if (arguments.InputDirectories.IsNullOrEmpty())
             {
                 throw new CommandLineArgumentException(
-                    $"{nameof(arguments.SourceDirectories)} is null or empty - please provide at least one source directory");
+                    $"{nameof(arguments.InputDirectories)} is null or empty - please provide at least one source directory");
             }
 
-            var doNotExist = arguments.SourceDirectories.Where(x => !x.Exists);
+            var doNotExist = arguments.InputDirectories.Where(x => !x.Exists);
             if (doNotExist.Any())
             {
                 throw new CommandLineArgumentException(
-                    $"The following directories given to {nameof(arguments.SourceDirectories)} do not exist: " + doNotExist.FormatList());
+                    $"The following directories given to {nameof(arguments.InputDirectories)} do not exist: " + doNotExist.FormatList());
             }
 
             if (arguments.OutputDirectory == null)
             {
-                arguments.OutputDirectory = arguments.SourceDirectories.First();
+                arguments.OutputDirectory = arguments.InputDirectories.First();
                 Log.Warn(
                     $"{nameof(arguments.OutputDirectory)} was not provided and was automatically set to source directory {arguments.OutputDirectory}");
             }
@@ -69,11 +65,11 @@ public static async Task<int> Execute(Arguments arguments)
 
             LoggedConsole.Write("Begin scanning directories");
 
-            var allIndexFiles = arguments.SourceDirectories.SelectMany(IndexGenerationData.FindAll);
+            var allIndexFiles = arguments.InputDirectories.SelectMany(IndexGenerationData.FindAll);
 
             if (allIndexFiles.IsNullOrEmpty())
             {
-                throw new MissingDataException($"Could not find `{IndexGenerationData.FileNameFragment}` files in:" + arguments.SourceDirectories.FormatList());
+                throw new MissingDataException($"Could not find `{IndexGenerationData.FileNameFragment}` files in:" + arguments.InputDirectories.FormatList());
             }
 
             Log.Debug("Checking files have dates");
@@ -142,7 +138,14 @@ void Add(string colorMap)
                 var midnight = arguments.Midnight == RibbonPlotDomain
                     ? string.Empty
                     : "Midnight=" + arguments.Midnight.Value.ToString("hhmm");
-                var path = FilenameHelpers.AnalysisResultPath(arguments.OutputDirectory, arguments.OutputDirectory.Name, "RibbonPlot", "png", colorMap, midnight);
+                var path = FilenameHelpers.AnalysisResultPath(
+                    arguments.OutputDirectory,
+                    arguments.OutputDirectory.Name,
+                    "RibbonPlot",
+                    "png",
+                    colorMap,
+                    midnight);
+
                 using (var file = File.Create(path))
                 {
                     image.SaveAsPng(file);

src/AnalysisPrograms/Production/Arguments/MainArgs.cs

@@ -8,6 +8,7 @@ namespace AnalysisPrograms.Production.Arguments
     using System.Threading.Tasks;
     using Acoustics.Shared;
     using AnalyseLongRecordings;
+    using AnalysisPrograms.Draw.RibbonPlots;
     using Draw.Zooming;
     using EventStatistics;
     using McMaster.Extensions.CommandLineUtils;
@@ -36,7 +37,7 @@ namespace AnalysisPrograms.Production.Arguments
     [Subcommand(ConcatenateIndexFiles.CommandName, typeof(ConcatenateIndexFiles.Arguments))]
     [Subcommand(DrawLongDurationSpectrograms.CommandName, typeof(DrawLongDurationSpectrograms.Arguments))]
     [Subcommand(DrawZoomingSpectrograms.CommandName, typeof(DrawZoomingSpectrograms.Arguments))]
-    [Subcommand(RibbonPlots.RibbonPlot.CommandName, typeof(RibbonPlots.RibbonPlot.Arguments))]
+    [Subcommand(RibbonPlot.CommandName, typeof(RibbonPlot.Arguments))]
     [Subcommand(DrawEasyImage.CommandName, typeof(DrawEasyImage.Arguments))]
     [Subcommand(Audio2InputForConvCnn.CommandName, typeof(Audio2InputForConvCnn.Arguments))]
     [Subcommand(DifferenceSpectrogram.CommandName, typeof(DifferenceSpectrogram.Arguments))]

src/AudioAnalysisTools/LongDurationSpectrograms/LDSpectrogramRGB.cs

@@ -65,6 +65,7 @@ namespace AudioAnalysisTools.LongDurationSpectrograms
     public class LDSpectrogramRGB
     {
         public const string SpectralRibbonTag = ".SpectralRibbon";
+        public const int RibbonPlotHeight = 32;
 
         // Below is some history about how indices were assigned to the RGB channels to make long-duration false-colour spectrograms
         // string[] keys = { "ACI", "TEN", "CVR", "BGN", "AVG", "VAR" }; // the OLDEST default i.e. used in 2014
@@ -1583,9 +1584,9 @@ public static Tuple<Image, string>[] DrawSpectrogramsFromSpectralIndices(
             //ribbon.Save(FilenameHelpers.AnalysisResultPath(outputDirectory, fileStem, colorMap2 + ".SummaryRibbon", "png"));
 
             // Spectrogram ribbons are very useful for viewing multiple days of recording.
-            var ribbon = cs1.GetSpectrogramRibbon(colorMap1, 32);
+            var ribbon = cs1.GetSpectrogramRibbon(colorMap1, RibbonPlotHeight);
             ribbon.Save(FilenameHelpers.AnalysisResultPath(outputDirectory, fileStem, colorMap1 + SpectralRibbonTag, "png"));
-            ribbon = cs1.GetSpectrogramRibbon(colorMap2, 32);
+            ribbon = cs1.GetSpectrogramRibbon(colorMap2, RibbonPlotHeight);
             ribbon.Save(FilenameHelpers.AnalysisResultPath(outputDirectory, fileStem, colorMap2 + SpectralRibbonTag, "png"));
 
             // only return images if chromeless

tests/Acoustics.Test/Acoustics.Test.csproj

@@ -103,12 +103,30 @@
     <Reference Include="Moq, Version=4.2.1502.911, Culture=neutral, PublicKeyToken=69f491c39445e920, processorArchitecture=MSIL">
       <HintPath>..\..\packages\Moq.4.2.1502.0911\lib\net40\Moq.dll</HintPath>
     </Reference>
+    <Reference Include="MoreLinq, Version=3.1.0.0, Culture=neutral, PublicKeyToken=384d532d7e88985d, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\morelinq.3.1.0\lib\net451\MoreLinq.dll</HintPath>
+    </Reference>
     <Reference Include="MSTestExtensions, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\..\packages\MSTestExtensions.4.0.0\lib\MSTestExtensions.dll</HintPath>
     </Reference>
     <Reference Include="Newtonsoft.Json, Version=11.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
       <HintPath>..\..\packages\Newtonsoft.Json.11.0.2\lib\net45\Newtonsoft.Json.dll</HintPath>
     </Reference>
+    <Reference Include="SixLabors.Core, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\SixLabors.Core.1.0.0-beta0007\lib\netstandard2.0\SixLabors.Core.dll</HintPath>
+    </Reference>
+    <Reference Include="SixLabors.Fonts, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\SixLabors.Fonts.1.0.0-beta0008\lib\netstandard2.0\SixLabors.Fonts.dll</HintPath>
+    </Reference>
+    <Reference Include="SixLabors.ImageSharp, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\SixLabors.ImageSharp.1.0.0-beta0006\lib\netstandard2.0\SixLabors.ImageSharp.dll</HintPath>
+    </Reference>
+    <Reference Include="SixLabors.ImageSharp.Drawing, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\SixLabors.ImageSharp.Drawing.1.0.0-beta0006\lib\netstandard2.0\SixLabors.ImageSharp.Drawing.dll</HintPath>
+    </Reference>
+    <Reference Include="SixLabors.Shapes, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\SixLabors.Shapes.1.0.0-beta0008\lib\netstandard2.0\SixLabors.Shapes.dll</HintPath>
+    </Reference>
     <Reference Include="SmartFormat, Version=2.1.0.2, Culture=neutral, PublicKeyToken=568866805651201f, processorArchitecture=MSIL">
       <HintPath>..\..\packages\SmartFormat.Net.2.1.0.2\lib\net45\SmartFormat.dll</HintPath>
     </Reference>
@@ -129,6 +147,9 @@
       <HintPath>..\..\packages\System.AppContext.4.3.0\lib\net46\System.AppContext.dll</HintPath>
       <Private>True</Private>
     </Reference>
+    <Reference Include="System.Buffers, Version=4.0.2.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\System.Buffers.4.4.0\lib\netstandard2.0\System.Buffers.dll</HintPath>
+    </Reference>
     <Reference Include="System.ComponentModel.Composition" />
     <Reference Include="System.ComponentModel.DataAnnotations" />
     <Reference Include="System.Configuration" />
@@ -140,6 +161,7 @@
       <RequiredTargetFramework>3.5</RequiredTargetFramework>
     </Reference>
     <Reference Include="System.Data" />
+    <Reference Include="System.Data.DataSetExtensions" />
     <Reference Include="System.Diagnostics.DiagnosticSource, Version=4.0.1.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
       <HintPath>..\..\packages\System.Diagnostics.DiagnosticSource.4.3.0\lib\net46\System.Diagnostics.DiagnosticSource.dll</HintPath>
     </Reference>
@@ -173,6 +195,9 @@
       <HintPath>..\..\packages\System.IO.FileSystem.Primitives.4.3.0\lib\net46\System.IO.FileSystem.Primitives.dll</HintPath>
       <Private>True</Private>
     </Reference>
+    <Reference Include="System.Memory, Version=4.0.1.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\System.Memory.4.5.1\lib\netstandard2.0\System.Memory.dll</HintPath>
+    </Reference>
     <Reference Include="System.Net" />
     <Reference Include="System.Net.Http">
       <HintPath>..\..\packages\System.Net.Http.4.3.0\lib\net46\System.Net.Http.dll</HintPath>
@@ -190,6 +215,9 @@
       <Private>True</Private>
     </Reference>
     <Reference Include="System.Numerics" />
+    <Reference Include="System.Numerics.Vectors, Version=4.1.4.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\System.Numerics.Vectors.4.5.0\lib\net46\System.Numerics.Vectors.dll</HintPath>
+    </Reference>
     <Reference Include="System.Reflection">
       <HintPath>..\..\packages\System.Reflection.4.3.0\lib\net462\System.Reflection.dll</HintPath>
       <Private>True</Private>
@@ -201,6 +229,9 @@
       <HintPath>..\..\packages\System.Runtime.4.3.0\lib\net462\System.Runtime.dll</HintPath>
       <Private>True</Private>
     </Reference>
+    <Reference Include="System.Runtime.CompilerServices.Unsafe, Version=4.0.4.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\System.Runtime.CompilerServices.Unsafe.4.5.1\lib\netstandard2.0\System.Runtime.CompilerServices.Unsafe.dll</HintPath>
+    </Reference>
     <Reference Include="System.Runtime.Extensions">
       <HintPath>..\..\packages\System.Runtime.Extensions.4.3.0\lib\net462\System.Runtime.Extensions.dll</HintPath>
       <Private>True</Private>
@@ -272,6 +303,7 @@
     <Compile Include="AnalysisPrograms\AcousticWorkbench.Orchestration\EventMetadataResolverTests.cs" />
     <Compile Include="AnalysisPrograms\AnalyzeLongRecordings\TestAnalyzeLongRecording.cs" />
     <Compile Include="AnalysisPrograms\Concatenation\ConcatenationTests.cs" />
+    <Compile Include="AnalysisPrograms\Draw\RibbonPlots\RibbonPlotTests.cs" />
     <Compile Include="AnalysisPrograms\Draw\Zooming\DrawZoomingTests.cs" />
     <Compile Include="AnalysisPrograms\MainEntryTests.cs" />
     <Compile Include="AnalysisPrograms\Production\FileSystemProviderTests.cs" />
@@ -302,12 +334,14 @@
     <Compile Include="RuntimesTests.cs" />
     <Compile Include="Shared\AppConfigHelperTests.cs" />
     <Compile Include="Shared\ConfigTests.cs" />
-    <Compile Include="Shared\Extensions\DateTimeAndTimeSpanExtensions.cs" />
+    <Compile Include="Shared\Extensions\DateTimeAndTimeSpanExtensionsTests.cs" />
     <Compile Include="Shared\LoggingTests\LoggingTests.cs" />
     <Compile Include="Shared\PathUtilsTests.cs" />
     <Compile Include="Shared\ProcessRunnerTests.cs" />
     <Compile Include="Shared\RangeTests.cs" />
     <Compile Include="TestHelpers\Factories\AudioRecordingFactory.cs" />
+    <Compile Include="TestHelpers\ImageHelpers.cs" />
+    <Compile Include="TestHelpers\TestImage.cs" />
     <Compile Include="TestHelpers\TestSetup.cs" />
     <Compile Include="Tools\AudioFilePreparerTests.cs" />
     <Compile Include="Shared\FileDateHelpersTests.cs" />