WIP for zooming spectrograms

Largely refactoring. Code is non functional at this point.

I did swap the underlying implementation for the Spectrogram matrix reading function. I covered it with unit tests to ensure compatibility.

Acoustics/Acoustics.Shared/AnalysisIo.cs

@@ -13,13 +13,24 @@ namespace Acoustics.Shared
 
     public class AnalysisIo
     {
-        public AnalysisIo(IFileSystem input, IFileSystem output, IFileSystem temp)
+        public AnalysisIo((IFileSystem FileSystem, FileSystemEntry Base) input, (IFileSystem FileSystem, DirectoryEntry Base) output, (IFileSystem FileSystem, DirectoryEntry Base)? temp)
         {
-            this.Input = input;
-            this.Output = output;
-            this.Temp = temp ?? input;
+            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; set; }
+
+        public DirectoryEntry OutputBase { get; set; }
+
+        public DirectoryEntry TempBase { get; set; }
+
         public IFileSystem Input { get; }
 
         public IFileSystem Output { get; }

Acoustics/Acoustics.Shared/Extensions/RandomExtensions.cs

@@ -1,10 +1,14 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
+// <copyright file="RandomExtensions.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.Extensions
 {
+    using System;
+    using System.Collections.Generic;
+    using System.Linq;
+    using System.Text;
+
     public static class RandomExtensions
     {
         public static Guid NextGuid(this Random random)
@@ -43,7 +47,25 @@ public static long NextLong(this Random random, long min, long max)
             random.NextBytes(buf);
             long longRand = BitConverter.ToInt64(buf, 0);
 
-            return (Math.Abs(longRand % (max - min)) + min);
+            return Math.Abs(longRand % (max - min)) + min;
+        }
+
+        public static double[,] NextMatrix(
+            this Random random,
+            int length,
+            int height)
+        {
+            var array = new double[length, height];
+
+            for (int i = 0; i < array.GetLength(0); i++)
+            {
+                for (int j = 0; j < array.GetLength(1); j++)
+                {
+                    array[i, j] = random.NextDouble();
+                }
+            }
+
+            return array;
         }
 
         public static DateTimeOffset NextDate(this Random random, DateTimeOffset? minimum = null, DateTimeOffset? maximum = null)

Acoustics/Acoustics.Shared/Extensions/ZioExtensions.cs

@@ -2,10 +2,12 @@
 // 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>
 
+// ReSharper disable once CheckNamespace
 namespace Zio
 {
     using System;
     using System.Collections.Generic;
+    using System.Drawing.Imaging;
     using System.IO;
     using System.Linq;
     using System.Text;
@@ -20,5 +22,54 @@ public static UPath ToUPath(this FileSystemInfo file)
         {
             return FileSystem.ConvertPathFromInternal(file.FullName);
         }
+
+        public static DirectoryEntry ToDirectoryEntry(this DirectoryInfo directory)
+        {
+            return new DirectoryEntry(FileSystem, directory.ToUPath());
+        }
+
+        public static DirectoryEntry ToFileEntry(this FileInfo file)
+        {
+            return new DirectoryEntry(FileSystem, file.ToUPath());
+        }
+
+        /// <summary>
+        /// Adapter method that converts a DirectoryInfo or FileInfo to a default Zio PhysicalFileSystem and equivalent
+        /// UPath.
+        /// </summary>
+        public static (IFileSystem FileSystem, UPath Path) ToZio(this FileSystemInfo file)
+        {
+            return (FileSystem, FileSystem.ConvertPathFromInternal(file.FullName));
+        }
+
+        /// <summary>
+        /// Return a default physical file system that can act as a crutch while we migrate
+        /// </summary>
+        /// <param name="path">Any UPath. This parameter has no effect.</param>
+        /// <returns>A stati</returns>
+        public static PhysicalFileSystem DefaultFileSystem(this UPath path)
+        {
+            return FileSystem;
+        }
+
+        public static void Save(this System.Drawing.Bitmap bitmap, IFileSystem fileSystem, UPath path)
+        {
+            var extension = path.GetExtensionWithDot();
+
+            ImageFormat format;
+            switch (extension)
+            {
+                case ".png":
+                    format = ImageFormat.Png;
+                    break;
+                default:
+                    throw new NotSupportedException();
+            }
+
+            using (var fileStream = fileSystem.CreateFile(path))
+            {
+                bitmap.Save(fileStream, format);
+            }
+        }
     }
 }

Acoustics/Acoustics.Test/Acoustics.Test.csproj

@@ -318,6 +318,7 @@
     <Compile Include="AudioAnalysisTools\EventStatistics\EventStatisticsCalculateTests.cs" />
     <Compile Include="AudioAnalysisTools\Indices\ClusterIndexTest.cs" />
     <Compile Include="AudioAnalysisTools\Indices\IndexCalculateTest.cs" />
+    <Compile Include="AudioAnalysisTools\Indices\IndexMatricesTests.cs" />
     <Compile Include="AudioAnalysisTools\LongDurationSpectrograms\LdSpectrogramConfigTests.cs" />
     <Compile Include="AudioAnalysisTools\LongDurationSpectrograms\LdSpectrogramStitchingTests.cs" />
     <Compile Include="AudioAnalysisTools\Oscillations2014\OscillationTests.cs" />

Acoustics/Acoustics.Test/AnalysisPrograms/Production/FileSystemProviderTests.cs

@@ -21,15 +21,15 @@ public class FileSystemProviderTests : OutputDirectoryTest
         [DataRow(null)]
         public void TestFullFileSystem(string path)
         {
-            var fs = FileSystemProvider.DetermineFileSystem(path);
+            var fs = FileSystemProvider.DetermineFileSystem(path).Item1;
 
             Assert.IsInstanceOfType(fs, typeof(PhysicalFileSystem));
         }
 
         [TestMethod]
         public void TestSubFileSystem()
         {
-            var fs = FileSystemProvider.DetermineFileSystem(this.outputDirectory.FullName);
+            var fs = FileSystemProvider.DetermineFileSystem(this.outputDirectory.FullName).Item1;
 
             Assert.IsInstanceOfType(fs, typeof(SubFileSystem));
 
@@ -40,7 +40,7 @@ public void TestSubFileSystem()
         public void TestSqliteFileSystem()
         {
             var path = this.outputDirectory.FullName + "\\test.sqlite3";
-            var fs = FileSystemProvider.DetermineFileSystem(path);
+            var fs = FileSystemProvider.DetermineFileSystem(path).Item1;
 
             Assert.IsInstanceOfType(fs, typeof(SqliteFileSystem));
 

Acoustics/Acoustics.Test/AudioAnalysisTools/Indices/IndexMatricesTests.cs

@@ -0,0 +1,59 @@
+// <copyright file="IndexMatricesTests.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.Test.AudioAnalysisTools.Indices
+{
+    using System;
+    using Acoustics.Shared.Csv;
+    using Acoustics.Shared.Extensions;
+    using global::AudioAnalysisTools.Indices;
+    using global::TowseyLibrary;
+    using Microsoft.VisualStudio.TestTools.UnitTesting;
+    using TestHelpers;
+
+    [TestClass]
+    public class IndexMatricesTests : OutputDirectoryTest
+    {
+        [TestMethod]
+        public void TestReadSpectrogram()
+        {
+            var testSpectra = PathHelper.ResolveAssetPath("20160725_203006_continuous1__Towsey.Acoustic.ACI.csv");
+
+            var matrix = IndexMatrices.ReadSpectrogram(testSpectra.ToFileInfo(), out var binCount);
+
+            Assert.AreEqual(30, matrix.GetLength(0));
+            Assert.AreEqual(256, matrix.GetLength(1));
+            Assert.AreEqual(256, binCount);
+
+            Assert.AreEqual(0.462924678189025, matrix[0, 0]);
+            Assert.AreEqual(0.42779069684277, matrix[0, 1]);
+            Assert.AreEqual(0.46412042529103, matrix[1, 0]);
+            Assert.AreEqual(0.444650614488611, matrix[1, 1]);
+        }
+
+        [TestMethod]
+        public void TestWriteReadSpectrogram()
+        {
+            var random = TestHelpers.Random.GetRandom();
+            var testSpectra = random.NextMatrix(100, 50);
+
+            var testFile = this.outputDirectory.CombineFile("test.matrix.csv");
+            Csv.WriteMatrixToCsv(testFile, testSpectra);
+
+            var matrix = IndexMatrices.ReadSpectrogram(testFile, out var binCount);
+
+            Assert.AreEqual(100, matrix.GetLength(0));
+            Assert.AreEqual(50, matrix.GetLength(1));
+            Assert.AreEqual(50, binCount);
+
+            var actualEnumerator = matrix.GetEnumerator();
+            foreach (var expected in testSpectra)
+            {
+                actualEnumerator.MoveNext();
+
+                Assert.AreEqual(expected, (double)actualEnumerator.Current, 1E-14, $"delta: {expected - (double)actualEnumerator.Current}");
+            }
+        }
+    }
+}

Acoustics/Acoustics.Test/AudioAnalysisTools/TileImage/AbsoluteDateTimeTilerTests.cs

@@ -8,6 +8,7 @@ namespace Acoustics.Test.AudioAnalysisTools.TileImage
     using global::AudioAnalysisTools.TileImage;
     using Microsoft.VisualStudio.TestTools.UnitTesting;
     using TestHelpers;
+    using Zio;
 
     [TestClass]
     public class AbsoluteDateTimeTilerTests
@@ -36,7 +37,7 @@ public void Setup()
             this.outputDirectory = PathHelper.GetTempDir();
 
             this.tiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 60.0 },
                 60.0,
@@ -80,7 +81,7 @@ public void TestItShouldCutAndPadRightWithTransparency()
         public void TestPaddingANonBlockTime()
         {
             this.tiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfileNotRoundStart,
                 new SortedSet<double>() { 60.0 },
                 60.0,

Acoustics/Acoustics.Test/AudioAnalysisTools/TileImage/TilerTests.cs

@@ -16,6 +16,7 @@ namespace Acoustics.Test.AudioAnalysisTools.TileImage
     using Microsoft.VisualStudio.TestTools.UnitTesting;
     using Moq;
     using TestHelpers;
+    using Zio;
 
     [TestClass]
     public class TilerTests
@@ -32,7 +33,7 @@ public void Setup()
             this.outputDirectory = PathHelper.GetTempDir();
 
             this.tiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 60.0, 24, 12, 6, 2, 1 },
                 60.0,
@@ -121,7 +122,7 @@ public void TestTileManyGroupsTilesByScaleAndSortsByOffset()
             List<ISuperTile> moqCurrent = new List<ISuperTile>(testCases.Length),
                              moqNext = new List<ISuperTile>(testCases.Length);
             var tilerMock = new Mock<Tiler>(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 60.0, 24, 12, 6, 2, 1 },
                 60.0,
@@ -139,17 +140,17 @@ public void TestTileManyGroupsTilesByScaleAndSortsByOffset()
 
             tilerMock.Object.TileMany(testCases);
 
-            const ISuperTile Empty = null;
+            const ISuperTile empty = null;
             var expected = new[]
                                {
-                                   Tuple.Create(Empty, testCases[5]), Tuple.Create(testCases[5], Empty),
-                                   Tuple.Create(Empty, Empty), Tuple.Create(Empty, testCases[0]),
-                                   Tuple.Create(testCases[0], testCases[1]), Tuple.Create(testCases[1], Empty),
-                                   Tuple.Create(Empty, Empty), Tuple.Create(Empty, testCases[4]),
+                                   Tuple.Create(empty, testCases[5]), Tuple.Create(testCases[5], empty),
+                                   Tuple.Create(empty, empty), Tuple.Create(empty, testCases[0]),
+                                   Tuple.Create(testCases[0], testCases[1]), Tuple.Create(testCases[1], empty),
+                                   Tuple.Create(empty, empty), Tuple.Create(empty, testCases[4]),
                                    Tuple.Create(testCases[4], testCases[3]), Tuple.Create(testCases[3], testCases[2]),
-                                   Tuple.Create(testCases[2], Empty), Tuple.Create(Empty, Empty),
-                                   Tuple.Create(Empty, testCases[6]), Tuple.Create(testCases[6], Empty),
-                                   Tuple.Create(Empty, Empty),
+                                   Tuple.Create(testCases[2], empty), Tuple.Create(empty, empty),
+                                   Tuple.Create(empty, testCases[6]), Tuple.Create(testCases[6], empty),
+                                   Tuple.Create(empty, empty),
                                };
 
             Assert.AreEqual(expected.Length, moqCurrent.Count);
@@ -426,7 +427,7 @@ public void EnsureSameTileNotRenderedTwice_ForWeirdlyOrderedResults()
 
             // scale size results in two images drawn
             var singleScaleTiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 0.16 },
                 60.0,
@@ -468,7 +469,7 @@ public void EnsureSameTileNotRenderedTwice_ForWeirdlyOrderedResultsReversed()
 
             // scale size results in two images drawn
             var singleScaleTiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 0.16 },
                 60.0,
@@ -507,7 +508,7 @@ public void EnsureSameThreeTilesWrittenForTwoOddlySizedSuperTiles()
                 };
 
             var singleScaleTiler = new Tiler(
-                this.outputDirectory,
+                this.outputDirectory.ToDirectoryEntry(),
                 this.tilingProfile,
                 new SortedSet<double>() { 0.16 },
                 60.0,