Set up Content Description as IAnalyzer2.

Issue #252

src/AnalysisConfigFiles/Towsey.ContentDescription.yml

@@ -0,0 +1,118 @@
+---
+# Summary: Calculates an acoustic signature for each minute of recording.
+#          An acoustic signature is a vector, ecah element of which is derived from a ContentDescription template.
+#
+#SegmentDuration: units=seconds;
+# Long duration recordings are cut into short segments for more efficient processing. Default segment length = 60 seconds.
+# WARNING: You should not change this property!!
+SegmentDuration: 60
+
+#SegmentOverlap: units=seconds;
+# WARNING: You should not change this property!!
+SegmentOverlap: 0
+
+# IndexCalculationDuration: units=seconds (default=60 seconds)
+# The Timespan (in seconds) over which summary and spectral indices are calculated
+# This value MUST not exceed value of SegmentDuration.
+# This Default value should not be changed.
+IndexCalculationDuration: 60.0
+
+# BgNoiseNeighborhood: units=seconds
+# By default, when IndexCalculationDuration = 60 seconds, background (stationary) noise is calculated from the full 60 second recording.
+BgNoiseNeighborhood: 5
+
+# By default, all recordings are down-sampled or up-sampled to 22050 Hz.
+# If you have a recording sampled at a higher rate, AND you wish to retain it, then set the correct value here.
+# Resample rate must be 2 X the desired Nyquist
+ResampleRate: 22050
+
+# FRAME LENGTH. units=samples
+# Typical value=512 where resample rate = 22050.
+# Frame Overlap is NEVER used when calculating acoustic indices.
+# This value should not be changed in order to retain consistency over multiple recordings.
+FrameLength: 512
+
+# Defining three frequency bands.
+# It is often useful to define three frequency bands, low, middle and high.
+# Six of the summary indices are calculated for the mid-band only.
+# This is useful to avoid low frequency anthropogenic noise and to target bird species which mostly sing in the 1-8 khz band.
+# The lower and upper bound of the mid-frequency band are set by LowFreqBound and HighFreqBound respectively.
+# Default values in code are LowFreqBound=1000Hz & MidFreqBound=8000
+LowFreqBound: 1000
+MidFreqBound: 8000
+HighFreqBound: 11000
+
+# The only FrequencyScale option currently available is only Linear
+FrequencyScale: Linear
+
+# SAVE INTERMEDIARY FILES
+# Available options (case-sensitive): [false/Never | true/Always | WhenEventsDetected]
+SaveIntermediateWavFiles: Never
+# If `true` saves a data into a seperate file every `SegmentDuration` seconds. Accepts a boolean value: [false|true]
+# If `true` saves a data into a seperate file every `SegmentDuration` seconds. Accepts a boolean value: [false|true]
+SaveIntermediateCsvFiles: false
+
+# SAVE INTERMEDIARY ONE-MINUTE (standard scale) SPECTROGRAMS
+# One-minute spectrograms can be saved in any analysis task.
+# Available options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
+SaveSonogramImages: Never
+
+# SAVE SONOGRAM DATA FILES FOR SUBSEQUENT ZOOMING SPECTROGRAMS
+# Next two parameters are used only when creating images for zooming spectrograms.
+# Warning: IndexCalculationDuration must be set = 0.2  when SaveSonogramData = true
+SaveSonogramData: false
+
+# TileImageOutput
+# if true an additional set of images will be produced that are tiles
+# if true, RequireDateInFilename must be set
+TileOutput: false
+
+# RequireDateInFilename:
+# 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.wav,  where +1000 is the time-zone offset for Brisbane.
+#     prefix_20140101T235959+Z.wav,     where +Z is the zero time-zone offset.
+#     prefix_20140101-235959+1000.wav
+#     prefix_20140101-235959+Z.wav
+# For more info on dates, see <dates.md> at https://github.com/QutEcoacoustics/audio-analysis/tree/master/docs
+RequireDateInFilename: false
+
+# Do NOT change following path. It is required for drawing false-colour spectrograms
+IndexPropertiesConfig: './IndexPropertiesConfig.yml'
+
+# EventThreshold: min value=0.0; max value=1.0.
+# This value can sometimes be used to manage the FP/FN trade-off performance of a call recogniser.
+# Not always used however.
+EventThreshold: 0.2
+
+# #############################################################################################################
+# The below parameters are used to configure drawing of the false-colour spectrograms
+# IMPORTANT NOTE: FC spectrograms are produced only IF the above IndexCalculationDuration := 60.0
+# Explanation of the FC configuration parameters is included below.
+LdSpectrogramConfig:
+    ColorMap1: "ACI-ENT-EVN"
+    ColorMap2: "BGN-PMN-EVN"
+
+    #EXPLANATION OF LDFC CONFIG PARAMETERS
+    # The ColourFilter parameter determines how much the low index values are emphasized or de-emphasized.
+    # The purpose is to make low intensity features stand out (emphasis) or become even less obvious (de-emphasis).
+    # This parameter applies a function that lies between y=x^-2 and y=x^2, i.e. between the square-root and the square.
+    # For an acoustic index value of X, newX = [(1/c - 1) * X^2 + X] * c, where c = the supplied filterCoeff.
+    #    When filterCoeff = 1.0, small values are maximally emphasized, i.e. y=sqrt(x).
+    #    When filterCoeff = 0.0, the matrix remains unchanged, that is, y=x.
+    #    When filterCoeff =-1.0, small values are maximally de-emphasized, i.e. y=x^2.
+    #    Generally usage suggests that a value of -0.25 is suitable. i.e. a slight de-emphasis.
+    ColourFilter: -0.25
+
+    # minutes x-axis scale
+    XAxisTicIntervalSeconds: 3600
+
+    # Hertz y-axis scale
+    # Only three option work now: "Linear", "Mel"' "Linear125Octaves7Tones28Nyquist32000" work at present
+    # Future options will be: Linear62Octaves31Nyquist11025, Linear125Octaves30Nyquist11025, Octaves24Nyquist32000
+    FreqScale: "Linear"
+    YAxisTicInterval: 1000
+...
+

src/AnalysisPrograms/AnalysisPrograms.csproj

@@ -302,6 +302,7 @@
     <Compile Include="..\AssemblyMetadata.cs">
       <Link>AssemblyMetadata.cs</Link>
     </Compile>
+    <Compile Include="ContentDescription.cs" />
     <Compile Include="AcousticWorkbench.Orchestration\EventMetadataResolver.cs" />
     <Compile Include="AcousticWorkbench.Orchestration\RemoteSegment.cs" />
     <Compile Include="AED.cs" />

src/AnalysisPrograms/ContentDescription.cs

@@ -0,0 +1,159 @@
+// <copyright file="ContentDescription.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
+{
+    using System;
+    using System.Collections.Generic;
+    using System.IO;
+    using System.Reflection;
+    using Acoustics.Shared;
+    using AnalysisBase;
+    using AnalysisBase.ResultBases;
+    using AudioAnalysisTools.Indices;
+    using AudioAnalysisTools.WavTools;
+    using log4net;
+
+    public class ContentDescription : AbstractStrongAnalyser
+    {
+        public const string AnalysisName = "ContentDescription";
+
+        // TASK IDENTIFIERS
+        //public const string TaskAnalyse = AnalysisName;
+        //public const string TaskLoadCsv = "loadCsv";
+        public const string TowseyAcoustic = "Towsey." + AnalysisName;
+
+        private static readonly ILog Log = LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
+
+        public const int ResampleRate = 17640;
+
+        public override string DisplayName => "Content Description";
+
+        public override string Identifier => TowseyAcoustic;
+
+        public override string Description => "[BETA] Generates six spectral indices for Content Description.";
+
+        public override AnalysisSettings DefaultSettings => new AnalysisSettings
+        {
+            AnalysisMaxSegmentDuration = TimeSpan.FromMinutes(1),
+            AnalysisMinSegmentDuration = TimeSpan.FromSeconds(30),
+            SegmentMediaType = MediaTypes.MediaTypeWav,
+            SegmentOverlapDuration = TimeSpan.Zero,
+            AnalysisTargetSampleRate = ResampleRate,
+        };
+
+        //public override void BeforeAnalyze(AnalysisSettings analysisSettings)
+        //{
+        //    var configuration = (AcousticIndices.AcousticIndicesConfig)analysisSettings.Configuration;
+
+        //    configuration.Validate(analysisSettings.AnalysisMaxSegmentDuration.Value);
+
+        //    analysisSettings.AnalysisAnalyzerSpecificConfiguration = configuration;
+        //}
+
+        //public static DescriptionResult Analysis(FileInfo segmentOfSourceFile, IDictionary<string, string> configDict, TimeSpan segmentStartOffset)
+        //{
+        //    var results = new DescriptionResult((int)Math.Floor(segmentStartOffset.TotalMinutes));
+        //    return results;
+        //}
+
+        /// <summary>
+        /// THis method calls others to do the work!.
+        /// TODO: SIMPLIFY THIS METHOD.
+        /// </summary>
+        public override AnalysisResult2 Analyze<T>(AnalysisSettings analysisSettings, SegmentSettings<T> segmentSettings)
+        {
+            //var acousticIndicesConfiguration = (AcousticIndices.AcousticIndicesConfig)analysisSettings.AnalysisAnalyzerSpecificConfiguration;
+            //var indexCalculationDuration = acousticIndicesConfiguration.IndexCalculationDuration.Seconds();
+
+            var config = new IndexCalculateConfig();
+            var indexCalculationDuration = TimeSpan.FromSeconds(60);
+
+            var audioFile = segmentSettings.SegmentAudioFile;
+            var recording = new AudioRecording(audioFile.FullName);
+            //var outputDirectory = segmentSettings.SegmentOutputDirectory;
+
+            // calculate indices for each one minute recording segment
+            IndexCalculateResult segmentResults = CalculateIndicesInOneMinuteSegmentOfRecording(
+                recording,
+                segmentSettings.SegmentStartOffset,
+                //segmentSettings.AnalysisIdealSegmentDuration,
+                indexCalculationDuration,
+                //acousticIndicesConfiguration.IndexProperties,
+                segmentSettings.Segment.SourceMetadata.SampleRate,
+                config);
+
+            //var trackScores = new List<Plot>(segmentResults.Length);
+            //var tracks = new List<SpectralTrack>(segmentResults.Length);
+
+            var analysisResults = new AnalysisResult2(analysisSettings, segmentSettings, recording.Duration)
+            {
+                AnalysisIdentifier = this.Identifier,
+                SpectralIndices = new SpectralIndexBase[1],
+            };
+            segmentResults.SpectralIndexValues.FileName = segmentSettings.Segment.SourceMetadata.Identifier;
+            analysisResults.SpectralIndices[0] = segmentResults.SpectralIndexValues;
+
+            /*
+            for (int i = 0; i < subsegmentResults.Length; i++)
+            {
+                var indexCalculateResult = segmentResults[i];
+                indexCalculateResult.SpectralIndexValues.FileName = segmentSettings.Segment.SourceMetadata.Identifier;
+
+                //analysisResults.SummaryIndices[i] = indexCalculateResult.SummaryIndexValues;
+                analysisResults.SpectralIndices[i] = indexCalculateResult.SpectralIndexValues;
+                //trackScores.AddRange(indexCalculateResult.TrackScores);
+                //if (indexCalculateResult.Tracks != null)
+                //{
+                //    tracks.AddRange(indexCalculateResult.Tracks);
+                //}
+            }
+            */
+
+            return analysisResults;
+        }
+
+        /// <summary>
+        /// TODO: REWRITE THIS METHOD.
+        /// </summary>
+        public static IndexCalculateResult CalculateIndicesInOneMinuteSegmentOfRecording(
+            AudioRecording recording,
+            TimeSpan segmentStartOffset,
+            TimeSpan indexCalculationDuration,
+            //Dictionary<string, IndexProperties> indexProperties,
+            int sampleRateOfOriginalAudioFile,
+            IndexCalculateConfig config)
+        {
+            //TODO: SET UP NEW class CalculateSizIndices.cs.
+            var resultsForSixIndices = IndexCalculate.Analysis(
+                recording,
+                segmentStartOffset,
+                null, //indexProperties,
+                sampleRateOfOriginalAudioFile,
+                segmentStartOffset,
+                config);
+
+            return resultsForSixIndices;
+        }
+
+        public override void WriteEventsFile(FileInfo destination, IEnumerable<EventBase> results)
+        {
+        }
+
+        public override void WriteSummaryIndicesFile(FileInfo destination, IEnumerable<SummaryIndexBase> results)
+        {
+        }
+
+        public override List<FileInfo> WriteSpectrumIndicesFiles(DirectoryInfo destination, string fileNameBase, IEnumerable<SpectralIndexBase> results)
+        {
+            var list = new List<FileInfo>();
+            return list;
+        }
+
+        public override void SummariseResults(AnalysisSettings settings, FileSegment inputFileSegment,
+            EventBase[] events, SummaryIndexBase[] indices, SpectralIndexBase[] spectralIndices, AnalysisResult2[] results)
+        {
+        }
+    }
+}

src/AnalysisPrograms/Sandpit.cs

@@ -64,11 +64,11 @@ public override Task<int> Execute(CommandLineApplication app)
                 Log.WriteLine("# Start Time = " + tStart.ToString(CultureInfo.InvariantCulture));
 
                 // CONTENT DESCRIPTION
-                ContentDescriptionCreateTemplates();
-                ContentDescriptionApplyTemplates();
+                //ContentDescriptionCreateTemplates();
+                //ContentDescriptionApplyTemplates();
 
                 //AnalyseFrogDataSet();
-                //Audio2CsvOverOneFile();
+                Audio2CsvOverOneFile();
                 //Audio2CsvOverMultipleFiles();
 
                 // used to get files from availae for Black rail and Least Bittern papers.
@@ -134,7 +134,7 @@ public static void ContentDescriptionApplyTemplates()
 
             var templatesFile = new FileInfo(@"C:\Ecoacoustics\ContentDescription\TemplateDefinitions.json");
             var listOfIndexFiles = new FileInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMezIndexFiles.txt");
-            var contentPlots = ContentDescription.ContentDescriptionOfMultipleRecordingFiles(listOfIndexFiles, templatesFile);
+            var contentPlots = AudioAnalysisTools.ContentDescriptionTools.ContentDescription.ContentDescriptionOfMultipleRecordingFiles(listOfIndexFiles, templatesFile);
 
             var images = GraphsAndCharts.DrawPlotDistributions(contentPlots);
             var plotsImage = ImageTools.CombineImagesVertically(images);
@@ -362,10 +362,16 @@ public static void Audio2CsvOverOneFile()
             //string configPath = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
             // Test on STANDARD 24-HOUR RECORDING
-            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652.wav";
+            //string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652+1000.wav";
             //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\14";
-            string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\Delete";
-            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
+            //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\Delete";
+            //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
+
+            // Test on Content Description
+            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652+1000.wav";
+            //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\14";
+            string outputPath = @"C:\Ecoacoustics\ContentDescription\TestOfSixIndices";
+            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.ContentDescription.yml";
 
             // Ivan Campos recordings
             //string recordingPath = @"G:\SensorNetworks\WavFiles\Ivancampos\INCIPO01_20161031_024006_898.wav";
@@ -428,7 +434,7 @@ public static void Audio2CsvOverOneFile()
             //string outputPath = @"C:\Ecoacoustics\Output\SERF\SERFIndicesNew_2013June19";
             //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
-          // USE 24-hour data or parts of from MEZ, TASMAn ISLAND, liz Znidersic
+            // USE 24-hour data or parts of from MEZ, TASMAn ISLAND, liz Znidersic
             // these are six hour recordings
             //string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_031652.wav";
             //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\04";