More work on zomming spectrograms

See #120 Tests pass. Writing images to Sqlite files seems to works. Now just running through bugs associated with tiles and super tiles. This patch: - Modifies the default zoomg spectrograms code for production settings - References SqliteFileSystem as a package so that dependencies are imported automatically - Fixes a few minor bugs
QutEcoacoustics · Nov 7, 2017 · e907eb6 · e907eb6
1 parent 1c43162
commit e907eb6
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Showing 11 changed files with 135 additions and 45 deletions.
diff --git a/Acoustics/Acoustics.Test/AnalysisPrograms/Draw/Zooming/DrawZoomingTests.cs b/Acoustics/Acoustics.Test/AnalysisPrograms/Draw/Zooming/DrawZoomingTests.cs
@@ -21,6 +21,9 @@ namespace Acoustics.Test.AnalysisPrograms.Draw.Zooming
     using Microsoft.VisualStudio.TestTools.UnitTesting;
     using TestHelpers;
 
+    using Zio;
+    using Zio.FileSystems.Community.SqliteFileSystem;
+
     [TestClass]
     public class DrawZoomingTests : OutputDirectoryTest
     {
@@ -41,9 +44,9 @@ public static void ClassInitialize(TestContext context)
             };
 
             context.WriteLine($"{DateTime.Now} generating indices fixture data");
-            MainEntry.SetLogVerbosity(LogVerbosity.Warn, true);
+            MainEntry.SetLogVerbosity(LogVerbosity.Warn, false);
             AnalyseLongRecording.Execute(arguments);
-            MainEntry.SetLogVerbosity(LogVerbosity.Debug, true);
+            MainEntry.SetLogVerbosity(LogVerbosity.Debug, false);
             context.WriteLine($"{DateTime.Now} finished generting fixture");
 
             ResultsDirectory = SharedDirectory.Combine("Towsey.Acoustic");
@@ -77,31 +80,47 @@ public void TestGenerateTiles()
                     ZoomAction = DrawZoomingSpectrograms.Arguments.ZoomActionType.Tile,
                 });
 
-            Assert.Fail();
+            var filesProduced = zoomOutput.EnumerateFiles().ToArray();
+
+            // there are 16 zoom levels, but the test recording is only 2min long
+            // at scale 240, we're rendering <1px of content and that tile is not generated
+            Assert.AreEqual(15, filesProduced.Length);
+
+            // not sure what else to test - generally exceptions should be thrown if anything goes wrong
         }
 
         /// <summary>
         /// Tests the rendering of zooming spectrograms for a minute of audio indices
         /// </summary>
         [TestMethod]
-        [Timeout(45_000)]
+        //[Timeout(45_000)]
         public void TestGenerateTilesSqlite()
         {
             // generate the zooming spectrograms
-            var zoomOutput = this.outputDirectory.CombineFile("Zooming/tiles.sqlite3");
+            var zoomOutput = this.outputDirectory.Combine("Zooming");
             DrawZoomingSpectrograms.Execute(
                 new DrawZoomingSpectrograms.Arguments()
                 {
                     Output = zoomOutput.FullName,
+                    OutputFormat = "sqlite3",
                     SourceDirectory = ResultsDirectory.FullName,
                     SpectrogramZoomingConfig = PathHelper.ResolveConfigFile("SpectrogramZoomingConfig.yml"),
                     ZoomAction = DrawZoomingSpectrograms.Arguments.ZoomActionType.Tile,
                 });
 
-            Assert.IsTrue(File.Exists(zoomOutput.FullName));
-            Assert.Fail();
-        }
+            var tiles = zoomOutput.CombineFile("OxleyCreek_site_1_1060_244333_20140529T081358+1000_120_0__Tiles.sqlite3");
+            Assert.IsTrue(tiles.Exists);
+
+            using (var fs = new SqliteFileSystem(tiles.FullName, OpenMode.ReadOnly))
+            {
+                var files = fs.EnumerateFiles(UPath.Root).ToArray();
 
-
+                // there are 16 zoom levels, but the test recording is only 2min long
+                // at scale 240, we're rendering <1px of content and that tile is not generated
+                Assert.AreEqual(15, files.Length);
+            }
+
+            // not sure what else to test - generally exceptions should be thrown if anything goes wrong
+        }
     }
 }
diff --git a/AudioAnalysis/AnalysisConfigFiles/SpectrogramZoomingConfig.yml b/AudioAnalysis/AnalysisConfigFiles/SpectrogramZoomingConfig.yml
@@ -1,33 +1,32 @@
 ---
 SpectralFrameDuration: 0.02
-TileWidth: 300
+TileWidth: 180
 # How to tile, valid values:
 # - PanoJsTilingProfile
 # - AbsoluteDateTilingProfile
 TilingProfile: AbsoluteDateTilingProfile
 SpectralIndexScale: 
+    - 240
+    - 120
     - 60
-    - 24
-    - 12
-    - 6
-    - 4
-    - 2
-    - 1
-    - 0.6
-    - 0.4
-    - 0.2
-SpectralFrameScale:
-    - 0.07
-    - 0.04
-    - 0.02
+    - 30
+    - 15
+    - 7.5
+    - 3.750
+    - 1.875
+    - 1.0
+    - 0.5
+    - 0.250
+    - 0.125
+SpectralFrameScale: []
 MaxTilesPerSuperTile: 12
 UseDistributionsForNormalization: false
 LdSpectrogramConfig:
     ColorMap1: "ACI-ENT-EVN" 
-    ColorMap2: "BGN-POW-EVN"
-    # minutes
+    ColorMap2: "BGN-PMN-EVN"
+    # seconds
     XAxisTicIntervalSeconds: 3600
     # Hertz
     YAxisTicInterval: 1000
-IndexPropertiesConfig: './IndexPropertiesConfig.yml'
+IndexPropertiesConfig: './IndexPropertiesConfig.HiRes.yml'
 ...
diff --git a/AudioAnalysis/AnalysisPrograms/AcousticIndices.cs b/AudioAnalysis/AnalysisPrograms/AcousticIndices.cs
@@ -500,6 +500,7 @@ public void SummariseResults(AnalysisSettings settings, FileSegment inputFileSeg
                     RecordingType = inputFileSegment.Source.Extension,
                     RecordingBasename = basename,
                     RecordingStartDate = inputFileSegment.TargetFileStartDate,
+                    RecordingDuration = inputFileSegment.TargetFileDuration.Value,
                     SampleRateOriginal = inputFileSegment.TargetFileSampleRate.Value,
                     SampleRateResampled = sampleRate,
                     FrameLength = frameWidth,

diff --git a/AudioAnalysis/AnalysisPrograms/AnalysisPrograms.csproj b/AudioAnalysis/AnalysisPrograms/AnalysisPrograms.csproj
@@ -175,6 +175,9 @@
       <HintPath>..\packages\MathNet.Numerics.2.6.2\lib\net40\MathNet.Numerics.dll</HintPath>
     </Reference>
     <Reference Include="Microsoft.CSharp" />
+    <Reference Include="Microsoft.Data.Sqlite, Version=2.0.0.0, Culture=neutral, PublicKeyToken=adb9793829ddae60, processorArchitecture=MSIL">
+      <HintPath>..\packages\Microsoft.Data.Sqlite.Core.2.0.0\lib\netstandard2.0\Microsoft.Data.Sqlite.dll</HintPath>
+    </Reference>
     <Reference Include="Microsoft.Threading.Tasks, Version=1.0.12.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a, processorArchitecture=MSIL">
       <HintPath>..\packages\Microsoft.Bcl.Async.1.0.168\lib\net40\Microsoft.Threading.Tasks.dll</HintPath>
     </Reference>
@@ -187,6 +190,21 @@
     <Reference Include="PowerArgs">
       <HintPath>..\..\Extra Assemblies\PowerArgs\PowerArgs.dll</HintPath>
     </Reference>
+    <Reference Include="SqliteFileSystem, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\SqliteFileSystem.1.0.0\lib\netstandard2.0\SqliteFileSystem.dll</HintPath>
+    </Reference>
+    <Reference Include="SQLitePCLRaw.batteries_green, Version=1.0.0.0, Culture=neutral, PublicKeyToken=a84b7dcfb1391f7f, processorArchitecture=MSIL">
+      <HintPath>..\packages\SQLitePCLRaw.bundle_green.1.1.7\lib\net45\SQLitePCLRaw.batteries_green.dll</HintPath>
+    </Reference>
+    <Reference Include="SQLitePCLRaw.batteries_v2, Version=1.0.0.0, Culture=neutral, PublicKeyToken=8226ea5df37bcae9, processorArchitecture=MSIL">
+      <HintPath>..\packages\SQLitePCLRaw.bundle_green.1.1.7\lib\net45\SQLitePCLRaw.batteries_v2.dll</HintPath>
+    </Reference>
+    <Reference Include="SQLitePCLRaw.core, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1488e028ca7ab535, processorArchitecture=MSIL">
+      <HintPath>..\packages\SQLitePCLRaw.core.1.1.7\lib\net45\SQLitePCLRaw.core.dll</HintPath>
+    </Reference>
+    <Reference Include="SQLitePCLRaw.provider.e_sqlite3, Version=1.0.0.0, Culture=neutral, PublicKeyToken=9c301db686d0bd12, processorArchitecture=MSIL">
+      <HintPath>..\packages\SQLitePCLRaw.provider.e_sqlite3.net45.1.1.7\lib\net45\SQLitePCLRaw.provider.e_sqlite3.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.ComponentModel.Composition" />
     <Reference Include="System.Configuration" />
@@ -221,8 +239,9 @@
       <HintPath>..\packages\Microsoft.Tpl.Dataflow.4.5.24\lib\portable-net45+win8+wpa81\System.Threading.Tasks.Dataflow.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="System.ValueTuple, Version=4.0.2.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
-      <HintPath>..\packages\System.ValueTuple.4.4.0-preview2-25405-01\lib\portable-net40+sl4+win8+wp8\System.ValueTuple.dll</HintPath>
+    <Reference Include="System.ValueTuple">
+      <HintPath>..\packages\System.ValueTuple.4.4.0\lib\net461\System.ValueTuple.dll</HintPath>
+      <Private>True</Private>
     </Reference>
     <Reference Include="System.Web" />
     <Reference Include="System.Web.Extensions" />
@@ -392,10 +411,6 @@
       <Project>{15741ead-ecd6-42f8-ab13-ea4ae636936e}</Project>
       <Name>QutBioacosutics.Xie</Name>
     </ProjectReference>
-    <ProjectReference Include="..\SqLiteFileSystem\SqliteFileSystem.csproj">
-      <Project>{364b812e-4e3d-415e-be10-2928028ee7b6}</Project>
-      <Name>SqliteFileSystem</Name>
-    </ProjectReference>
     <ProjectReference Include="..\TowseyLibrary\TowseyLibrary.csproj">
       <Project>{7c6831fd-f60c-4f7b-8e6a-35e850174411}</Project>
       <Name>TowseyLibrary</Name>
@@ -517,6 +532,12 @@
     </PropertyGroup>
     <Error Condition="!Exists('..\packages\MSBuildTasks.1.5.0.235\build\MSBuildTasks.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\MSBuildTasks.1.5.0.235\build\MSBuildTasks.targets'))" />
     <Error Condition="!Exists('..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets'))" />
+    <Error Condition="!Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.linux.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.linux.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\SQLitePCLRaw.lib.e_sqlite3.linux.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.linux.targets'))" />
+    <Error Condition="!Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.osx.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.osx.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\SQLitePCLRaw.lib.e_sqlite3.osx.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.osx.targets'))" />
+    <Error Condition="!Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.v110_xp.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.v110_xp.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\SQLitePCLRaw.lib.e_sqlite3.v110_xp.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.v110_xp.targets'))" />
   </Target>
   <Import Project="..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets" Condition="Exists('..\packages\Microsoft.Bcl.Build.1.0.21\build\Microsoft.Bcl.Build.targets')" />
+  <Import Project="..\packages\SQLitePCLRaw.lib.e_sqlite3.linux.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.linux.targets" Condition="Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.linux.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.linux.targets')" />
+  <Import Project="..\packages\SQLitePCLRaw.lib.e_sqlite3.osx.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.osx.targets" Condition="Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.osx.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.osx.targets')" />
+  <Import Project="..\packages\SQLitePCLRaw.lib.e_sqlite3.v110_xp.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.v110_xp.targets" Condition="Exists('..\packages\SQLitePCLRaw.lib.e_sqlite3.v110_xp.1.1.7\build\net35\SQLitePCLRaw.lib.e_sqlite3.v110_xp.targets')" />
 </Project>
diff --git a/AudioAnalysis/AnalysisPrograms/Draw/Zooming/DrawZoomingSpectrograms.cs b/AudioAnalysis/AnalysisPrograms/Draw/Zooming/DrawZoomingSpectrograms.cs
@@ -62,7 +62,7 @@ public static void Execute(Arguments arguments)
             // create file systems for reading input and writing output
             var io = FileSystemProvider.GetInputOutputFileSystems(
                 arguments.SourceDirectory,
-                FileSystemProvider.MakePath(arguments.Output, common.OriginalBasename, arguments.OutputFormat))
+                FileSystemProvider.MakePath(arguments.Output, common.OriginalBasename, arguments.OutputFormat, "Tiles"))
                 .EnsureInputIsDirectory();
 
             switch (arguments.ZoomAction)

diff --git a/AudioAnalysis/AnalysisPrograms/Production/FileSystemProvider.cs b/AudioAnalysis/AnalysisPrograms/Production/FileSystemProvider.cs
@@ -77,6 +77,9 @@ public static (IFileSystem, DirectoryEntry) DetermineFileSystem(string path, boo
             }
             else
             {
+                // ensure parent directory exists on disk
+                Directory.CreateDirectory(Path.GetDirectoryName(path));
+
                 switch (extension)
                 {
                     case "." + SqlitePattern:
@@ -104,7 +107,7 @@ public static AnalysisIo GetInputOutputFileSystems(string inputPath, string outp
             return new AnalysisIo(input, output, null);
         }
 
-        public static string MakePath(string directory, string baseName, string format)
+        public static string MakePath(string directory, string baseName, string format, string tag)
         {
             if (string.IsNullOrEmpty(format))
             {
@@ -113,7 +116,7 @@ public static string MakePath(string directory, string baseName, string format)
 
             Contract.Requires(AllFormats.Contains(format));
 
-            return Path.Combine(directory, baseName + "." + format);
+            return Path.Combine(directory, FilenameHelpers.AnalysisResultName(baseName, tag, format));
         }
     }
 

diff --git a/AudioAnalysis/AnalysisPrograms/Production/MainEntryUtilities.cs b/AudioAnalysis/AnalysisPrograms/Production/MainEntryUtilities.cs
@@ -479,7 +479,7 @@ private static void ModifyVerbosity(MainEntryArguments arguments)
             SetLogVerbosity(arguments.LogLevel, arguments.QuietConsole);
         }
 
-        public static void SetLogVerbosity(LogVerbosity logVerbosity, bool quietConsole)
+        public static void SetLogVerbosity(LogVerbosity logVerbosity, bool quietConsole = false)
         {
             Level modifiedLevel;
             switch (logVerbosity)

diff --git a/AudioAnalysis/AnalysisPrograms/packages.config b/AudioAnalysis/AnalysisPrograms/packages.config
@@ -11,11 +11,20 @@
   <package id="Microsoft.Bcl" version="1.1.10" targetFramework="net40" requireReinstallation="true" />
   <package id="Microsoft.Bcl.Async" version="1.0.168" targetFramework="net40" />
   <package id="Microsoft.Bcl.Build" version="1.0.21" targetFramework="net40" />
+  <package id="Microsoft.Data.Sqlite" version="2.0.0" targetFramework="net462" />
+  <package id="Microsoft.Data.Sqlite.Core" version="2.0.0" targetFramework="net462" />
   <package id="Microsoft.Net.Http" version="2.2.29" targetFramework="net40" requireReinstallation="true" />
   <package id="Microsoft.Tpl.Dataflow" version="4.5.24" targetFramework="net452" />
   <package id="MSBuildTasks" version="1.5.0.235" targetFramework="net40" developmentDependency="true" />
+  <package id="SqliteFileSystem" version="1.0.0" targetFramework="net462" />
+  <package id="SQLitePCLRaw.bundle_green" version="1.1.7" targetFramework="net462" />
+  <package id="SQLitePCLRaw.core" version="1.1.7" targetFramework="net462" />
+  <package id="SQLitePCLRaw.lib.e_sqlite3.linux" version="1.1.7" targetFramework="net462" />
+  <package id="SQLitePCLRaw.lib.e_sqlite3.osx" version="1.1.7" targetFramework="net462" />
+  <package id="SQLitePCLRaw.lib.e_sqlite3.v110_xp" version="1.1.7" targetFramework="net462" />
+  <package id="SQLitePCLRaw.provider.e_sqlite3.net45" version="1.1.7" targetFramework="net462" />
   <package id="StyleCop.Analyzers" version="1.1.0-beta004" targetFramework="net40" developmentDependency="true" />
-  <package id="System.ValueTuple" version="4.4.0-preview2-25405-01" targetFramework="net40" requireReinstallation="true" />
+  <package id="System.ValueTuple" version="4.4.0" targetFramework="net462" />
   <package id="YamlDotNet" version="3.9.0" targetFramework="net40" />
   <package id="Zio" version="0.3.1" targetFramework="net462" />
 </packages>
diff --git a/AudioAnalysis/AudioAnalysisTools/Indices/IndexGenerationData.cs b/AudioAnalysis/AudioAnalysisTools/Indices/IndexGenerationData.cs
@@ -82,6 +82,8 @@ public IndexGenerationData()
 
         public string RecordingBasename { get; set; }
 
+        public TimeSpan RecordingDuration { get; set; }
+
         /// <summary>
         /// Returns the index generation data from file in passed directory.
         /// </summary>

diff --git a/AudioAnalysis/AudioAnalysisTools/LongDurationSpectrograms/Zooming/ZoomTiledSpectrograms.cs b/AudioAnalysis/AudioAnalysisTools/LongDurationSpectrograms/Zooming/ZoomTiledSpectrograms.cs
@@ -42,7 +42,7 @@ public static void DrawTiles(
             var zoomConfig = common.SpectrogramZoomingConfig;
             LdSpectrogramConfig ldsConfig = common.SpectrogramZoomingConfig.LdSpectrogramConfig;
             var distributions = common.IndexDistributions;
-            var indexGeneration = common.IndexGenerationData;
+            var indexGenerationData = common.IndexGenerationData;
             var indexProperties = common.IndexProperties;
 
             string fileStem = common.OriginalBasename;
@@ -60,7 +60,7 @@ public static void DrawTiles(
                     " we need at least some scales to render zooming spectrograms");
             }
 
-            var shouldRenderStandardScale = standardScales.IsNullOrEmpty();
+            var shouldRenderStandardScale = !standardScales.IsNullOrEmpty();
             if (shouldRenderStandardScale)
             {
                 Log.Warn("Standard spectrograms will not be rendered");
@@ -71,7 +71,7 @@ public static void DrawTiles(
             Log.Info("Tiling at scales: " + allImageScales.ToCommaSeparatedList());
 
             // determine what naming format to use for tiles
-            var namingPattern = GetTilingProfile(common, zoomConfig, indexGeneration);
+            var namingPattern = GetTilingProfile(common, zoomConfig, indexGenerationData);
 
             // pad out image so it produces a whole number of tiles
             // this solves the asymmetric right padding of short audio files
@@ -93,12 +93,31 @@ public static void DrawTiles(
             // TODO: does this load all spectra? even ones we don't need...
             var (spectra, filteredIndexProperties) = LoadSpectra(io, analysisTag, fileStem, indexProperties);
 
-            GenerateIndexSpectrogramTiles(indexScales, ldsConfig, filteredIndexProperties, zoomConfig, spectra, indexGeneration, fileStem, namingPattern, tiler);
+            // false color index tiles
+            GenerateIndexSpectrogramTiles(
+                indexScales,
+                ldsConfig,
+                filteredIndexProperties,
+                zoomConfig,
+                spectra,
+                indexGenerationData,
+                fileStem,
+                namingPattern,
+                tiler);
 
-            // ####################### DRAW ZOOMED-IN SPECTROGRAMS FROM STANDARD SPECTRAL FRAMES
+            // standard fft frame spectrograms
             if (shouldRenderStandardScale)
             {
-                GenerateStandardSpectrogramTiles(spectra, indexGeneration, ldsConfig, filteredIndexProperties, zoomConfig, standardScales, fileStem, namingPattern, tiler);
+                GenerateStandardSpectrogramTiles(
+                    spectra,
+                    indexGenerationData,
+                    ldsConfig,
+                    filteredIndexProperties,
+                    zoomConfig,
+                    standardScales,
+                    fileStem,
+                    namingPattern,
+                    tiler);
             }
 
             Log.Success("Tiling complete");
@@ -185,7 +204,7 @@ private static void GenerateIndexSpectrogramTiles(
             Dictionary<string, IndexProperties> filteredIndexProperties,
             SpectrogramZoomingConfig zoomConfig,
             Dictionary<string, double[,]> spectra,
-            IndexGenerationData indexGeneration,
+            IndexGenerationData indexGenerationData,
             string fileStem,
             TilingProfile namingPattern,
             Tiler tiler)
@@ -196,14 +215,23 @@ private static void GenerateIndexSpectrogramTiles(
             foreach (double scale in indexScales)
             {
                 Log.Info("Starting scale: " + scale);
+
+                if (indexGenerationData.RecordingDuration.TotalSeconds < scale)
+                {
+                    Log.Warn($"Skipping scale step {scale} because recording duration ({indexGenerationData.RecordingDuration}) is less than 1px of scale");
+                    continue;
+                }
+
+                // TODO: eventual optimisation, remove concept of super tiles
+                // TODO: optimisation, cache aggregation layers (currently every layer is raggregated from base level)
                 TimeSpan imageScale = TimeSpan.FromSeconds(scale);
                 var superTiles = DrawSuperTilesAtScaleFromIndexSpectrograms(
                     ldsConfig,
                     filteredIndexProperties,
                     zoomConfig,
                     imageScale,
                     spectra,
-                    indexGeneration,
+                    indexGenerationData,
                     fileStem,
                     namingPattern.ChromeOption);