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Content description now works using IAnalyzer2
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Issue #252 Content description now working through IAnalyzer2 architecture.
But much cleaning up work needs to be done.
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@towsey
towsey committed Oct 20, 2019
1 parent b3e568e commit a52c9b0
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Showing 4 changed files with 197 additions and 125 deletions.
1 change: 1 addition & 0 deletions src/AnalysisConfigFiles/Towsey.ContentDescription.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
# 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.
#
AnalysisName: ContentDescription
#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!!
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172 changes: 101 additions & 71 deletions src/AnalysisPrograms/ContentDescription.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,16 @@ namespace AnalysisPrograms
{
using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.Drawing;
using System.Globalization;
using System.IO;
using System.Linq;
using System.Reflection;
using Acoustics.Shared;
using Acoustics.Shared.ConfigFile;
using Acoustics.Shared.Csv;
using AnalysisBase;
using AnalysisBase.ResultBases;
using AudioAnalysisTools;
using AudioAnalysisTools.ContentDescriptionTools;
using AudioAnalysisTools.Indices;
using AudioAnalysisTools.LongDurationSpectrograms;
using AudioAnalysisTools.WavTools;
Expand Down Expand Up @@ -69,7 +67,7 @@ public override void BeforeAnalyze(AnalysisSettings analysisSettings)
[Serializable]
public class CdConfig : IndexCalculateConfig
{
private LdSpectrogramConfig ldfcsConfig = new LdSpectrogramConfig();
//private LdSpectrogramConfig ldfcsConfig = new LdSpectrogramConfig();

/// <summary>
/// Gets or sets the LDFC spectrogram configuration.
Expand All @@ -83,16 +81,14 @@ public class CdConfig : IndexCalculateConfig
public override AnalysisResult2 Analyze<T>(AnalysisSettings analysisSettings, SegmentSettings<T> segmentSettings)
{
//var cdConfiguration = (IndexCalculateConfig)analysisSettings.AnalysisAnalyzerSpecificConfiguration;
var cdConfiguration = analysisSettings.AnalysisAnalyzerSpecificConfiguration;
//var cdConfiguration = analysisSettings.AnalysisAnalyzerSpecificConfiguration;
//var indexCalculationDuration = cdConfiguration.IndexCalculationDuration.Seconds();
//var outputDirectory = segmentSettings.SegmentOutputDirectory;
var indexProperties = IndexCalculateSixOnly.GetIndexProperties();

var config = new IndexCalculateConfig();
var indexCalculationDuration = TimeSpan.FromSeconds(60);

var indexCalculationDuration = TimeSpan.FromSeconds(60); //default value for content description
var audioFile = segmentSettings.SegmentAudioFile;
var recording = new AudioRecording(audioFile.FullName);
var outputDirectory = segmentSettings.SegmentOutputDirectory;

var segmentResults = IndexCalculateSixOnly.Analysis(
recording,
Expand Down Expand Up @@ -155,28 +151,17 @@ public override void SummariseResults(AnalysisSettings settings, FileSegment inp
//var cdConfig = (CdConfig)settings.AnalysisAnalyzerSpecificConfiguration;

var sourceAudio = inputFileSegment.Source;
var resultsDirectory = AnalysisCoordinator.GetNamedDirectory(settings.AnalysisOutputDirectory, this);
//var frameWidth = cdConfig.FrameLength;
var frameWidth = 512;
int sampleRate = 22050;

//int sampleRate = AppConfigHelper.DefaultTargetSampleRate;
//sampleRate = cdConfig.ResampleRate ?? sampleRate;

// Gather settings for rendering false color spectrograms
//var ldSpectrogramConfig = cdConfig.LdSpectrogramConfig;
var ldSpectrogramConfig = new LdSpectrogramConfig();

string basename = Path.GetFileNameWithoutExtension(sourceAudio.Name);
var resultsDirectory = AnalysisCoordinator.GetNamedDirectory(settings.AnalysisOutputDirectory, this);
var frameWidth = 512; //default value which should not be changed
frameWidth = settings.Configuration.GetIntOrNull(AnalysisKeys.FrameLength) ?? frameWidth;
var frameStep = frameWidth;
int sampleRate = 22050; //default value which should not be changed
sampleRate = settings.Configuration.GetIntOrNull(AnalysisKeys.ResampleRate) ?? sampleRate;

var indexCalculationDurationTimeSpan = TimeSpan.FromSeconds(60);
var bgNoiseBuffer = TimeSpan.FromSeconds(5);
// output to disk (so other analyzers can use the data,
// output to disk so other analyzers can use the data,
// only data - configuration settings that generated these indices
// this data can then be used by post-process analyses
/* NOTE: The value for FrameStep is used only when calculating a standard spectrogram
* FrameStep is NOT used when calculating Spectral indices.
*/
var indexConfigData = new IndexGenerationData()
{
RecordingExtension = inputFileSegment.Source.Extension,
Expand All @@ -186,15 +171,13 @@ public override void SummariseResults(AnalysisSettings settings, FileSegment inp
SampleRateOriginal = inputFileSegment.TargetFileSampleRate.Value,
SampleRateResampled = sampleRate,
FrameLength = frameWidth,
FrameStep = settings.Configuration.GetIntOrNull(AnalysisKeys.FrameStep) ?? frameWidth,
//IndexCalculationDuration = cdConfig.IndexCalculationDurationTimeSpan,
//BgNoiseNeighbourhood = cdConfig.BgNoiseBuffer,
IndexCalculationDuration = indexCalculationDurationTimeSpan,
BgNoiseNeighbourhood = bgNoiseBuffer,
FrameStep = frameStep,
IndexCalculationDuration = TimeSpan.FromSeconds(60), // default value for content description
BgNoiseNeighbourhood = TimeSpan.FromSeconds(5), // default value for content description
AnalysisStartOffset = inputFileSegment.SegmentStartOffset ?? TimeSpan.Zero,
MaximumSegmentDuration = settings.AnalysisMaxSegmentDuration,
BackgroundFilterCoeff = SpectrogramConstants.BACKGROUND_FILTER_COEFF,
LongDurationSpectrogramConfig = ldSpectrogramConfig,
LongDurationSpectrogramConfig = new LdSpectrogramConfig(),
};
var icdPath = FilenameHelpers.AnalysisResultPath(
resultsDirectory,
Expand All @@ -212,50 +195,51 @@ public override void SummariseResults(AnalysisSettings settings, FileSegment inp
// Calculate the index distribution statistics and write to a json file. Also save as png image
var indexDistributions = IndexDistributions.WriteSpectralIndexDistributionStatistics(dictionaryOfSpectra, resultsDirectory, basename);

// Draw ldfc spectrograms
Tuple<Image, string>[] images =
// Draw ldfc spectrograms and return path to 2maps image.
string ldfcSpectrogramPath =
DrawSpectrogramsFromSpectralIndices(
inputDirectory: resultsDirectory,
outputDirectory: resultsDirectory,
ldSpectrogramConfig: ldSpectrogramConfig,
indexGenerationData: indexConfigData,
basename: basename,
analysisType: this.Identifier,
indexSpectrograms: dictionaryOfSpectra,
imageChrome: true.ToImageChrome());
indexSpectrograms: dictionaryOfSpectra);

// now get the content description for each minute.
//FileInfo templatesFile = settings.ConfigFile; //TODO TODO TODO TODO
FileInfo templatesFile = new FileInfo(@"C:\Ecoacoustics\ContentDescription\TemplateDefinitions.json");
var contentPlots = GetContentDescription(spectralIndices, templatesFile);
//TODO TODO TODO TODO
string directoryPath = @"C:\Ecoacoustics\ContentDescription\TestOfSixIndices\Towsey.ContentDescription";
var images = GraphsAndCharts.DrawPlotDistributions(contentPlots);
var plotsImage = ImageTools.CombineImagesVertically(images);
var path1 = Path.Combine(directoryPath, "ScoreDistributions.png");
plotsImage.Save(path1);

//TODO TODO TODO TODO
// Attach content description plots to LDFC spectrogram and write to file
var ldfcSpectrogram = Image.FromFile(ldfcSpectrogramPath);
var image = ContentVisualization.DrawLdfcSpectrogramWithContentScoreTracks(ldfcSpectrogram, contentPlots);
var path2 = Path.Combine(directoryPath, "Testing_2Maps.CONTENTnew08.png");
image.Save(path2);
}

/// <summary>
/// This IS THE MAJOR STATIC METHOD FOR CREATING LD SPECTROGRAMS
/// IT CAN BE COPIED AND APPROPRIATELY MODIFIED BY ANY USER FOR THEIR OWN PURPOSE.
/// WARNING: Make sure the parameters in the CONFIG file are consistent with the CSV files.
/// This is cut down version of the method of same name in LDSpectrogramRGB.cs.
/// </summary>
/// <param name="inputDirectory">inputDirectory</param>
/// <param name="outputDirectory">outputDirectory</param>
/// <param name="ldSpectrogramConfig">config for drawing FCSs</param>
/// <param name="indexGenerationData">indexGenerationData</param>
/// <param name="basename">stem name of the original recording</param>
/// <param name="analysisType">will usually be "Towsey.Acoustic"</param>
/// <param name="indexSpectrograms">Optional spectra to pass in. If specified the spectra will not be loaded from disk! </param>
/// <param name="imageChrome">If true, this method generates and returns separate chromeless images used for tiling website images.</param>
public static Tuple<Image, string>[] DrawSpectrogramsFromSpectralIndices(
DirectoryInfo inputDirectory,
/// <param name="outputDirectory">outputDirectory.</param>
/// <param name="indexGenerationData">indexGenerationData.</param>
/// <param name="basename">stem name of the original recording.</param>
/// <param name="indexSpectrograms">Optional spectra to pass in. If specified the spectra will not be loaded from disk!.</param>
private static string DrawSpectrogramsFromSpectralIndices(
DirectoryInfo outputDirectory,
LdSpectrogramConfig ldSpectrogramConfig,
//FileInfo indexPropertiesConfigPath,
IndexGenerationData indexGenerationData,
string basename,
string analysisType,
Dictionary<string, double[,]> indexSpectrograms = null,
ImageChrome imageChrome = ImageChrome.With)
Dictionary<string, double[,]> indexSpectrograms = null)
{
var config = ldSpectrogramConfig;

// These parameters manipulate the colour map and appearance of the false-colour spectrogram
string colorMap1 = SpectrogramConstants.RGBMap_ACI_ENT_EVN;
string colorMap2 = SpectrogramConstants.RGBMap_BGN_PMN_EVN;
string colorMap2 = SpectrogramConstants.RGBMap_BGN_PMN_OSC;

// Set ColourFilter: Must lie between +/-1. A good value is -0.25
// Set Color Filter: Must lie between +/-1. A good value is -0.25
var config = new LdSpectrogramConfig();
if (config.ColourFilter == null)
{
config.ColourFilter = SpectrogramConstants.BACKGROUND_FILTER_COEFF;
Expand All @@ -279,13 +263,11 @@ public static Tuple<Image, string>[] DrawSpectrogramsFromSpectralIndices(

// following line is debug purposes only
//cs.StartOffset = cs.StartOffset + TimeSpan.FromMinutes(15);

var indexProperties = IndexCalculateSixOnly.GetIndexProperties();
cs1.SetSpectralIndexProperties(indexProperties);

// Load the Index Spectrograms into a Dictionary
cs1.LoadSpectrogramDictionary(indexSpectrograms);

if (cs1.GetCountOfSpectrogramMatrices() == 0)
{
Log.Error("No spectrogram matrices in the dictionary. Spectrogram files do not exist?");
Expand All @@ -296,19 +278,67 @@ public static Tuple<Image, string>[] DrawSpectrogramsFromSpectralIndices(
var keys = indexProperties.Keys.ToArray();
cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);

// create two false-colour spectrogram images
// create two false-color spectrogram images
var image1NoChrome = cs1.DrawFalseColourSpectrogramChromeless(cs1.ColorMode, colorMap1);
var image2NoChrome = cs1.DrawFalseColourSpectrogramChromeless(cs1.ColorMode, colorMap2);
var spacer = new Bitmap(image1NoChrome.Width, 10);
var imageList = new[] { image1NoChrome, spacer, image2NoChrome };
var imageList = new[] { image1NoChrome, spacer, image2NoChrome, spacer};
Image image3 = ImageTools.CombineImagesVertically(imageList);
var outputPath = FilenameHelpers.AnalysisResultPath(outputDirectory, fileStem, "2Maps", "png");
image3.Save(outputPath);
return outputPath;
}

/// <summary>
/// Calculate the content description for each minute.
/// </summary>
/// <param name="spectralIndices">set of spectral indices for each minute.</param>
/// <param name="templatesFile">json file containing description of templates.</param>
public static List<Plot> GetContentDescription(SpectralIndexBase[] spectralIndices, FileInfo templatesFile)
{
// Read in the content description templates
var templates = Json.Deserialize<TemplateManifest[]>(templatesFile);
var templatesAsDictionary = DataProcessing.ExtractDictionaryOfTemplateDictionaries(templates);
//TODO need to get start time of recording as Minute of the Day
var elapsedTimeAtStartOfRecording = 0; //TODO TODO TODO

// create dictionary of index vectors
var results = new List<DescriptionResult>();

int length = spectralIndices.Length;

//loop over all minutes in the recording
for (int i = 0; i < length; i++)
{
var oneMinuteOfIndices = spectralIndices[i];

// Transfer acoustic indices to dictionary
var indicesDictionary = IndexCalculateSixOnly.ConvertIndicesToDictionary(oneMinuteOfIndices);

//TODO TODO Remove next line and change the template manifest to indicate what indices are to be used.
indicesDictionary.Remove("OSC");

// scan templates over one minute of indices
var resultsForOneMinute = AudioAnalysisTools.ContentDescriptionTools.ContentDescription.AnalyzeOneMinute(
templates,
templatesAsDictionary,
indicesDictionary,
elapsedTimeAtStartOfRecording + i);
results.Add(resultsForOneMinute);
}

var plotDict = DataProcessing.ConvertResultsToPlots(results, 1440, 0);
var contentPlots = DataProcessing.ConvertPlotDictionaryToPlotList(plotDict);

// convert scores to z-scores
//contentPlots = DataProcessing.SubtractMeanPlusSd(contentPlots);

//the following did not work as well.
//contentPlots = DataProcessing.SubtractModeAndSd(contentPlots);

// only return images if chromeless
return imageChrome == ImageChrome.Without
? new[] { Tuple.Create(image1NoChrome, colorMap1), Tuple.Create(image2NoChrome, colorMap2) }
: null;
// Use percentile thresholding followed by normalize in 0,1.
contentPlots = DataProcessing.PercentileThresholding(contentPlots, 90);
return contentPlots;
}
}
}
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