Create spectrogram from standardizedfeaturesextraction

-Created configuration file for SFE
-Fixed bug for empty/null configfile
-Create spectrogram within SFE

Acoustics/Acoustics.Shared/ConfigFile/ConfigFile.cs

@@ -143,6 +143,11 @@ public static FileInfo ResolveConfigFile(FileInfo file, params DirectoryInfo[] s
 
         public static FileInfo ResolveConfigFile(string file, params DirectoryInfo[] searchPaths)
         {
+            if (file.IsNullOrEmpty())
+            {
+                throw new ArgumentException("Try to resolve config failed, because supplied file argument was null or empty.", nameof(file));
+            }
+
             var success = TryResolveConfigFile(file, searchPaths.Select(x => x.ToDirectoryEntry()), out FileEntry configFile);
 
             if (success)

AudioAnalysis/AnalysisConfigFiles/Ecosounds.StandardizedFeatures.yml

@@ -0,0 +1,54 @@
+---
+# Summary: Calculates standardized features for machine learning tasks
+
+AnalysisName: Ecosounds.StandardizedFeatures
+#SegmentDuration: units=minutes;
+SegmentDuration: 1
+#SegmentOverlap: units=seconds;
+SegmentOverlap: 0
+
+# BgNoiseNeighbourhood: units=seconds (default IndexCalculationDuration = 60 seconds)
+# BG noise for any location is calculated by extending the region of index calculation from 5 seconds before start to 5 sec after end of current index interval.
+#    Ten seconds is considered a minimum interval to obtain a reliable estimate of BG noise.
+#    The  BG noise interval is not extended beyond start or end of recording segment.
+#    Consequently for a 60sec Index calculation duration, the  BG noise is calculated form the 60sec segment only.
+BgNoiseNeighbourhood: 5
+
+# Resample rate must be 2 X the desired Nyquist
+ResampleRate: 22050
+
+# FRAME LENGTH. units=samples
+# FrameWidth is used without overlap to calculate the spectral indices. Typical value=512
+FrameLength: 512
+
+
+#Default values in code are LowFreqBound=1000Hz & MidFreqBound=8000
+LowFreqBound: 1000
+MidFreqBound: 8000
+HighFreqBound: 11000
+
+# FrequencyScale options are currently only Linear and Octave
+# Octave scale is to be used only for Jasco Marine recordings @ sample rate = 64000
+FrequencyScale: Linear
+
+# SAVE INTERMEDIARY FILES
+# Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+SaveIntermediateWavFiles: Never
+SaveIntermediateCsvFiles: false
+# One-minute spectrograms can be saved in any analysis task.
+# Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+SaveSonogramImages: Never
+
+# if true, an unambiguous date time must be provided in the source file's name.
+# if true, an exception will be thrown if no such date is found
+# if false, and a valid date is still found in file name, it will still be parsed
+# supports formats like:
+#     prefix_20140101T235959+1000.mp3
+#     prefix_20140101T235959+Z.mp3
+#     prefix_20140101-235959+1000.mp3
+#     prefix_20140101-235959+Z.mp3
+RequireDateInFilename: false
+
+IndexPropertiesConfig: './IndexPropertiesConfig.yml'
+...
+

AudioAnalysis/AnalysisPrograms/AnalysisPrograms.csproj

@@ -285,7 +285,7 @@
     <Compile Include="SourcePreparers\RemoteSourcePreparer.cs" />
     <Compile Include="SourcePreparers\LocalSourcePreparer.cs" />
     <Compile Include="SourcePreparers\RemoteSourcePreparerException.cs" />
-    <Compile Include="StandardizedFeatureExtraction.cs" />
+    <Compile Include="StandardizedFeatures\StandardizedFeatureExtraction.cs" />
     <Compile Include="SURFAnalysis.cs" />
     <Compile Include="OscillationsGeneric.cs" />
     <Compile Include="DifferenceSpectrogram.cs" />
@@ -415,6 +415,7 @@
     <Analyzer Include="..\packages\StyleCop.Analyzers.1.1.0-beta004\analyzers\dotnet\cs\StyleCop.Analyzers.CodeFixes.dll" />
     <Analyzer Include="..\packages\StyleCop.Analyzers.1.1.0-beta004\analyzers\dotnet\cs\StyleCop.Analyzers.dll" />
   </ItemGroup>
+  <ItemGroup />
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

AudioAnalysis/AnalysisPrograms/Production/Actions.cs

@@ -23,7 +23,7 @@ namespace AnalysisPrograms.Production
     using EventStatistics;
     using PowerArgs;
     using Recognizers.Base;
-    using StandardizedFeatureExtraction;
+    using StandardizedFeatures;
 
     /// <summary>
     /// Defines the various actions (sub programs) that we can run.
@@ -227,7 +227,7 @@ public static Action<object> TruskingerFelt()
         public StandardizedFeatureExtraction.Arguments StandardizedFeatureExtractionArgs { get; set; }
         public static Action<StandardizedFeatureExtraction.Arguments> StandardizedFeatureExtraction()
         {
-            return AnalysisPrograms.StandardizedFeatureExtraction.StandardizedFeatureExtraction.Execute;
+            return StandardizedFeatures.StandardizedFeatureExtraction.Execute;
         }
 
         [ArgDescription("Calls SnrAnalysis.Execute():  Calculates signal to noise ratio.")]

AudioAnalysis/AnalysisPrograms/StandardizedFeatures/StandardizedFeatureExtraction.cs

@@ -0,0 +1,146 @@
+// <copyright file="StandardizedFeatureExtraction.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 AnalysisPrograms.StandardizedFeatures
+{
+    using System;
+    using System.Collections.Generic;
+    using System.Drawing.Imaging;
+    using System.IO;
+    using System.Security.Policy;
+    using Acoustics.Shared;
+    using Acoustics.Shared.ConfigFile;
+    using AnalysisBase;
+    using AnalysisBase.ResultBases;
+    using AudioAnalysisTools;
+    using AudioAnalysisTools.DSP;
+    using AudioAnalysisTools.Indices;
+    using AudioAnalysisTools.WavTools;
+    using log4net.Repository.Hierarchy;
+    using PowerArgs;
+    using TowseyLibrary;
+
+    public class StandardizedFeatureExtraction : AbstractStrongAnalyser
+    {
+        private const string Sentence = "Hello World";
+
+        // Input is a class object of Arguments, class is made below
+        public static void Execute(Arguments arguments)
+        {
+            for (int i = 0; i < arguments.Multiplication; i++)
+            {
+                Console.WriteLine(Sentence);
+            }
+        }
+
+        // Creates a class that constructs arguments, the description is shown in help StandardizedFeatureExtraction
+        // The variable Multiplication can later be used
+        public class Arguments
+        {
+            [ArgDescription("How many times hello world")]
+            public int Multiplication { get; set; }
+        }
+
+        // Implemented from AbstractStrongAnalyser
+        public override string DisplayName
+        {
+            get { return "Standardized Feature Extraction"; }
+        }
+
+        public override string Identifier
+        {
+            get { return "Ecosounds.StandardizedFeatures"; }
+        }
+
+        public virtual string Description
+        {
+            get { return "Performs a standardized feature extraction."; }
+        }
+
+        public override AnalysisResult2 Analyze<T>(AnalysisSettings analysisSettings, SegmentSettings<T> segmentSettings)
+        {
+            var audioFile = segmentSettings.SegmentAudioFile;
+            var recording = new AudioRecording(audioFile.FullName);
+            var outputDirectory = segmentSettings.SegmentOutputDirectory;
+            //int sampleRate = recording.WavReader.SampleRate;
+
+            var analysisResults = new AnalysisResult2(analysisSettings, segmentSettings, recording.Duration);
+
+            // Convert the dynamic config to IndexCalculateConfig class and merge in the unnecesary parameters.
+            IndexCalculateConfig config = IndexCalculateConfig.GetConfig(analysisSettings.Configuration, false);
+
+            int frameSize = config.FrameLength;
+            int frameStep = frameSize;
+            //var indexCalculationDuration = config.IndexCalculationDuration;
+
+            //// get duration in seconds and sample count and frame count
+            //double subsegmentDurationInSeconds = indexCalculationDuration.TotalSeconds;
+            //int subsegmentSampleCount = (int)(subsegmentDurationInSeconds * sampleRate);
+            //double subsegmentFrameCount = subsegmentSampleCount / (double)frameStep;
+            //subsegmentFrameCount = (int)Math.Ceiling(subsegmentFrameCount);
+
+            //// In order not to lose the last fractional frame, round up the frame number
+            //// and get the exact number of samples in the integer number of frames.
+            //// Do this because when IndexCalculationDuration = 100ms, the number of frames is only 8.
+            //subsegmentSampleCount = (int)(subsegmentFrameCount * frameStep);
+
+            //// get start and end samples of the subsegment and noise segment
+            //double localOffsetInSeconds = segmentSettings.SegmentStartOffset.TotalSeconds;
+            //int startSample = (int)(localOffsetInSeconds * sampleRate);
+            //int endSample = startSample + subsegmentSampleCount - 1;
+
+            // Default behaviour: set SUBSEGMENT = total recording
+            AudioRecording subsegmentRecording = recording;
+
+            //double[] subsamples = DataTools.Subarray(recording.WavReader.Samples, startSample, subsegmentSampleCount);
+            //var wr = new Acoustics.Tools.Wav.WavReader(subsamples, 1, 16, sampleRate);
+            //subsegmentRecording = new AudioRecording(wr);
+
+            // EXTRACT ENVELOPE and SPECTROGRAM FROM SUBSEGMENT
+            var dspOutput1 = DSP_Frames.ExtractEnvelopeAndFfts(subsegmentRecording, frameSize, frameStep);
+
+            analysisSettings.AnalysisImageSaveBehavior = SaveBehavior.Always;
+
+            if (analysisSettings.AnalysisImageSaveBehavior.ShouldSave())
+            {
+                string imagePath = Path.Combine(outputDirectory.FullName, segmentSettings.SegmentImageFile.Name);
+
+                //prepare amplitude spectrogram
+                double[,] amplitudeSpectrogramData = dspOutput1.AmplitudeSpectrogram; // get amplitude spectrogram.
+                var image = ImageTools.DrawReversedMatrix(MatrixTools.MatrixRotate90Anticlockwise(amplitudeSpectrogramData));
+                image.Save(imagePath, ImageFormat.Png);
+                analysisResults.ImageFile = new FileInfo(imagePath);
+            }
+            //image.Save(@"C:\Work\Output\testimage.png", ImageFormat.Png);
+
+            return analysisResults;
+        }
+
+        public override void WriteEventsFile(FileInfo destination, IEnumerable<EventBase> results)
+        {
+            throw new NotImplementedException();
+        }
+
+        public override void WriteSummaryIndicesFile(FileInfo destination, IEnumerable<SummaryIndexBase> results)
+        {
+            throw new NotImplementedException();
+        }
+
+        public override List<FileInfo> WriteSpectrumIndicesFiles(DirectoryInfo destination, string fileNameBase, IEnumerable<SpectralIndexBase> results)
+        {
+            throw new NotImplementedException();
+        }
+
+        public override void SummariseResults(
+            AnalysisSettings settings,
+            FileSegment inputFileSegment,
+            EventBase[] events,
+            SummaryIndexBase[] indices,
+            SpectralIndexBase[] spectralIndices,
+            AnalysisResult2[] results)
+        {
+            // no op
+        }
+    }
+}