Merge pull request #137 from QutBioacoustics/zoom-refactor

Zooming index spectrograms improvments
Original hash: 83642c7

Acoustics/Acoustics.Shared/Acoustics.Shared.csproj

@@ -10,7 +10,7 @@
     <AppDesignerFolder>Properties</AppDesignerFolder>
     <RootNamespace>Acoustics.Shared</RootNamespace>
     <AssemblyName>Acoustics.Shared</AssemblyName>
-    <TargetFrameworkVersion>v4.5.2</TargetFrameworkVersion>
+    <TargetFrameworkVersion>v4.6.2</TargetFrameworkVersion>
     <FileAlignment>512</FileAlignment>
     <SolutionDir Condition="$(SolutionDir) == '' Or $(SolutionDir) == '*Undefined*'">..\..\EcoSounds\</SolutionDir>
     <TargetFrameworkProfile />
@@ -203,10 +203,11 @@
     <Reference Include="System.Core" />
     <Reference Include="System.Data.Linq" />
     <Reference Include="System.Drawing" />
+    <Reference Include="System.IO.Compression" />
     <Reference Include="System.Net" />
     <Reference Include="System.Runtime.Serialization" />
     <Reference Include="System.ValueTuple, Version=4.0.2.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
-      <HintPath>..\..\AudioAnalysis\packages\System.ValueTuple.4.4.0-preview2-25405-01\lib\netstandard1.0\System.ValueTuple.dll</HintPath>
+      <HintPath>..\..\AudioAnalysis\packages\System.ValueTuple.4.4.0-preview2-25405-01\lib\net461\System.ValueTuple.dll</HintPath>
     </Reference>
     <Reference Include="System.Web" />
     <Reference Include="System.Web.Extensions" />
@@ -220,8 +221,12 @@
     <Reference Include="YamlDotNet.Dynamic">
       <HintPath>..\..\Extra Assemblies\YamlDotNet\YamlDotNet.Dynamic.dll</HintPath>
     </Reference>
+    <Reference Include="Zio, Version=0.3.6.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\AudioAnalysis\packages\Zio.0.3.6\lib\net45\Zio.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
+    <Compile Include="AnalysisIo.cs" />
     <Compile Include="AppConfigHelper.cs" />
     <Compile Include="Base58.cs" />
     <Compile Include="Binary.cs" />
@@ -257,6 +262,7 @@
     <Compile Include="Extensions\StringCaseExtensions.cs" />
     <Compile Include="Extensions\TaskExtensions.cs" />
     <Compile Include="Extensions\TupleExtensions.cs" />
+    <Compile Include="Extensions\ZioExtensions.cs" />
     <Compile Include="FileDateHelpers.cs" />
     <Compile Include="FileNameHelpers.cs" />
     <Compile Include="Formatters.cs" />
@@ -275,7 +281,6 @@
     <Compile Include="PropertyComparer.cs" />
     <Compile Include="Range.cs" />
     <Compile Include="ResultProperty.cs" />
-    <Compile Include="SqlServerTypes\Loader.cs" />
     <Compile Include="StatDescriptive.cs" />
     <Compile Include="StringKeyValueStore.cs" />
     <Compile Include="TempFileHelper.cs" />

Acoustics/Acoustics.Shared/AnalysisIo.cs

@@ -0,0 +1,66 @@
+// <copyright file="AnalysisIo.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
+{
+    using System;
+    using System.Collections.Generic;
+    using System.Linq;
+    using System.Text;
+    using System.Threading.Tasks;
+
+    using Acoustics.Shared.Contracts;
+
+    using Zio;
+
+    public class AnalysisIo
+    {
+        public AnalysisIo((IFileSystem FileSystem, FileSystemEntry Base) input, (IFileSystem FileSystem, DirectoryEntry Base) output, (IFileSystem FileSystem, DirectoryEntry Base)? temp)
+        {
+            this.Input = input.FileSystem;
+            this.InputBase = input.Base;
+
+            this.Output = output.FileSystem;
+            this.OutputBase = output.Base;
+
+            this.Temp = (temp ?? input).FileSystem;
+            this.TempBase = (DirectoryEntry)(temp ?? input).Base;
+        }
+
+        public FileSystemEntry InputBase { get; }
+
+        public DirectoryEntry OutputBase { get; }
+
+        public DirectoryEntry TempBase { get; }
+
+        public IFileSystem Input { get; }
+
+        public IFileSystem Output { get; }
+
+        public IFileSystem Temp { get; }
+
+        public AnalysisIoInputDirectory EnsureInputIsDirectory()
+        {
+            Contract.Requires(this.InputBase != null, $"{nameof(this.InputBase)} must not be null");
+
+            if (this.Input.DirectoryExists(this.InputBase.Path))
+            {
+                return new AnalysisIoInputDirectory((this.Input, this.InputBase), (this.Output, this.OutputBase), (this.Temp, this.TempBase));
+            }
+
+            throw new ArgumentException($"Expected `{this.InputBase}` to be a directory, but it is not");
+        }
+    }
+
+    public class AnalysisIoInputDirectory
+        : AnalysisIo
+    {
+        internal AnalysisIoInputDirectory((IFileSystem FileSystem, FileSystemEntry Base) input, (IFileSystem FileSystem, DirectoryEntry Base) output, (IFileSystem FileSystem, DirectoryEntry Base)? temp)
+            : base(input, output, temp)
+        {
+        }
+
+        public new DirectoryEntry InputBase => (DirectoryEntry)base.InputBase;
+    }
+}

Acoustics/Acoustics.Shared/AppConfigHelper.cs

@@ -30,7 +30,10 @@ public static class AppConfigHelper
         /// </summary>
         public const string Iso8601FileCompatibleDateFormat = "yyyyMMddTHHmmsszzz";
 
+        public const string Iso8601FileCompatibleDateFormatUtcWithFractionalSeconds = "yyyyMMddTHHmmss.FFF\\Z";
+
         public const string StandardDateFormatUtc = "yyyyMMdd-HHmmssZ";
+
         public const string StandardDateFormatUtcWithFractionalSeconds = "yyyyMMdd-HHmmss.FFFZ";
 
         public static string FileDateFormatUtc

Acoustics/Acoustics.Shared/Base58.cs

@@ -1,4 +1,8 @@
-namespace Acoustics.Shared
+// <copyright file="Base58.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
 {
     using System;
 

Acoustics/Acoustics.Shared/ConfigFile/ConfigFile.cs

@@ -11,6 +11,7 @@ namespace Acoustics.Shared.ConfigFile
 {
     using System;
     using System.Collections.Generic;
+    using System.Diagnostics;
     using System.IO;
     using System.Linq;
     using System.Reflection;
@@ -19,6 +20,8 @@ namespace Acoustics.Shared.ConfigFile
     using YamlDotNet.Dynamic;
     using YamlDotNet.RepresentationModel;
 
+    using Zio;
+
     public static class ConfigFile
     {
         public const string ProfilesKey = "Profiles";
@@ -46,10 +49,7 @@ public static string ConfigFolder
                     $"Cannot find currently set ConfigFiles directory. {defaultConfigFolder} does not exist!");
             }
 
-            set
-            {
-                defaultConfigFolder = value;
-            }
+            set => defaultConfigFolder = value;
         }
 
         public static dynamic GetProfile(dynamic configuration, string profileName)
@@ -143,12 +143,11 @@ public static FileInfo ResolveConfigFile(FileInfo file, params DirectoryInfo[] s
 
         public static FileInfo ResolveConfigFile(string file, params DirectoryInfo[] searchPaths)
         {
-            FileInfo configFile;
-            var success = TryResolveConfigFile(file, searchPaths, out configFile);
+            var success = TryResolveConfigFile(file, searchPaths.Select(x => x.ToDirectoryEntry()), out FileEntry configFile);
 
             if (success)
             {
-                return configFile;
+                return configFile.ToFileInfo();
             }
 
             var searchedIn =
@@ -159,44 +158,48 @@ public static FileInfo ResolveConfigFile(string file, params DirectoryInfo[] sea
             throw new ConfigFileException(message, file);
         }
 
-        public static bool TryResolveConfigFile(string file, DirectoryInfo[] searchPaths, out FileInfo configFile)
+        public static bool TryResolveConfigFile(string file, IEnumerable<DirectoryEntry> searchPaths, out FileEntry configFile)
         {
             configFile = null;
             if (string.IsNullOrWhiteSpace(file))
             {
                 return false;
             }
 
-            if (File.Exists(file))
+            // this is a holdover from concrete file systems. The concept of a working directory has no real
+            // equivalent in a virtual file system but this is implemented for compatibility
+            // GetFullPath should take care of relative paths relative to current working directory
+            var fullPath = Path.GetFullPath(file);
+            if (File.Exists(fullPath))
             {
-                configFile = new FileInfo(file);
+                configFile = fullPath.ToFileEntry();
                 return true;
             }
 
-            // if it does not exist
-            // and is rooted, it can't exist
             if (Path.IsPathRooted(file))
             {
+                // if absolute on concrete file system and can't be found then we can't resolve automatically
                 return false;
             }
 
-            if (searchPaths != null && searchPaths.Length > 0)
+            if (searchPaths != null)
             {
-                foreach (var directoryInfo in searchPaths)
+                foreach (var directory in searchPaths)
                 {
-                    var searchPath = Path.GetFullPath(Path.Combine(directoryInfo.FullName, file));
-                    if (File.Exists(searchPath))
+                    var searchPath = directory.CombineFile(file);
+                    if (searchPath.Exists)
                     {
-                        configFile = new FileInfo(searchPath);
+                        configFile = searchPath;
                         return true;
                     }
                 }
             }
 
+            // config files are always packaged with the app so use a physical file system
             var defaultConfigFile = Path.GetFullPath(Path.Combine(ConfigFolder, file));
             if (File.Exists(defaultConfigFile))
             {
-                configFile = new FileInfo(defaultConfigFile);
+                configFile = defaultConfigFile.ToFileEntry();
                 return true;
             }
 
@@ -206,7 +209,7 @@ public static bool TryResolveConfigFile(string file, DirectoryInfo[] searchPaths
                 var nestedDefaultConfigFile = Path.Combine(directory, file);
                 if (File.Exists(nestedDefaultConfigFile))
                 {
-                    configFile = new FileInfo(nestedDefaultConfigFile);
+                    configFile = nestedDefaultConfigFile.ToFileEntry();
                     return true;
                 }
             }

Acoustics/Acoustics.Shared/Contracts/Contract.cs

@@ -19,6 +19,22 @@ namespace Acoustics.Shared.Contracts
     /// </summary>
     public class Contract
     {
+        /// <summary>
+        /// Require the supplied value to be not null, otherwise throw a argument null exception.
+        /// </summary>
+        /// <param name="value">Whether or not the exception should be thrown</param>
+        /// <param name="name">The name of the argument that was null</param>
+        /// <param name="message">The message to add to the exception if the check fails</param>
+        [DebuggerHidden]
+        [ContractAnnotation("value:null => halt")]
+        public static void RequiresNotNull(object value, string name = "", string message = "Precondition failed - value was null")
+        {
+            if (value == null)
+            {
+                throw new ArgumentNullException(name, message);
+            }
+        }
+
         /// <summary>
         /// Require the supplied boolean to be true, otherwise throw an exception.
         /// </summary>

Acoustics/Acoustics.Shared/Csv/Csv.cs

@@ -25,6 +25,8 @@ namespace Acoustics.Shared.Csv
     using Fasterflect;
     using log4net;
 
+    using Zio;
+
     /// <summary>
     /// Generic methods for reading and writing Csv file.
     /// .
@@ -242,6 +244,7 @@ private static List<T[]> DecodeMatrix<T>(this CsvReader reader, bool includeRowI
             {
                 throw new CsvHelperException("Expected an index header and there was none");
             }
+
             if (!includeRowIndex && headers[0] == "Index")
             {
                 throw new CsvHelperException("Did not expect an index header and there was one");
@@ -276,36 +279,44 @@ private static List<T[]> DecodeMatrix<T>(this CsvReader reader, bool includeRowI
             int columnCount;
             var csvRows = DecodeMatrix<T>(reader, includeRowIndex, out rowCount, out columnCount);
 
-            var result = dimensionality == TwoDimensionalArray.RowMajor
+            var result = dimensionality == TwoDimensionalArray.None
                 ? new T[rowCount, columnCount]
                 : new T[columnCount, rowCount];
 
-            for (int i = 0; i < csvRows.Count; i++)
+            for (int r = 0; r < csvRows.Count; r++)
             {
-                var row = csvRows[i];
-                for (int j = 0; j < row.Length; j++)
+                var row = csvRows[r];
+                for (int c = 0; c < row.Length; c++)
                 {
                     switch (dimensionality)
                     {
-                        case TwoDimensionalArray.RowMajor:
-                            result[i, j] = row[j];
+                        case TwoDimensionalArray.None:
+                            result[r, c] = row[c];
                             break;
-                        case TwoDimensionalArray.ColumnMajor:
-                            result[j, i] = row[j];
+                        case TwoDimensionalArray.Transpose:
+                            result[c, r] = row[c];
                             break;
-                        case TwoDimensionalArray.ColumnMajorFlipped:
-                            result[columnCount - 1 - j, i] = row[j];
+                        case TwoDimensionalArray.Rotate90ClockWise:
+                            // note these operations are reversed and look wrong, but because they
+                            // are being done on the LHS of assignment, the operations need to be inversed
+                            result[c, rowCount - 1 - r] = row[c];
+                            break;
+                        case TwoDimensionalArray.Rotate90AntiClockWise:
+                            // note these operations are reversed and look wrong, but because they
+                            // are being done on the LHS of assignment, the operations need to be inversed
+                            result[columnCount - 1 - c, r] = row[c];
+
                             break;
                         default:
                             throw new NotImplementedException("Other dimensionalities not implemented");
                     }
                 }
             }
+
             return result;
         }
 
-
-        public static void WriteMatrixToCsv<T>(FileInfo destination, T[,] matrix, TwoDimensionalArray dimensionality = TwoDimensionalArray.RowMajor)
+        public static void WriteMatrixToCsv<T>(FileInfo destination, T[,] matrix, TwoDimensionalArray dimensionality = TwoDimensionalArray.None)
         {
             Contract.Requires(destination != null);
 
@@ -320,16 +331,20 @@ public static void WriteMatrixToCsv<T>(FileInfo destination, T[,] matrix, TwoDim
             }
         }
 
-        public static T[,] ReadMatrixFromCsv<T>(FileInfo source, TwoDimensionalArray dimensionality = TwoDimensionalArray.RowMajor)
+        public static T[,] ReadMatrixFromCsv<T>(FileInfo source, TwoDimensionalArray transform = TwoDimensionalArray.None)
+        {
+            return ReadMatrixFromCsv<T>(source.ToFileEntry(), transform);
+        }
+
+        public static T[,] ReadMatrixFromCsv<T>(FileEntry source, TwoDimensionalArray transform = TwoDimensionalArray.None)
         {
             Contract.Requires(source != null);
 
-            // not tested!
             using (var stream = source.OpenText())
             {
                 var reader = new CsvReader(stream, DefaultConfiguration);
 
-                return reader.DecodeMatrix<T>(dimensionality, true);
+                return reader.DecodeMatrix<T>(transform, true);
             }
         }