Skip to content

Commit

Permalink
Generalise OSC index
Browse files Browse the repository at this point in the history 
Generalise the OSC index code so that it can be calculated for recordings of reduced length i.e. for anywhere in the pyramid stack.
It works well for the longer recordings but not so well for recordings < 1.0 seconds long.
  • Loading branch information
@towsey @atruskie
towsey authored and atruskie committed Dec 19, 2018
1 parent bc09ebd commit 2eeeb44
Show file tree
Hide file tree
Showing 8 changed files with 472 additions and 301 deletions.
97 changes: 81 additions & 16 deletions src/AudioAnalysisTools/Oscillations2014.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,10 @@ public class FreqVsOscillationsResult
public static void TESTMETHOD_DrawOscillationSpectrogram()
{
{
var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds30to32.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds45to46.wav".ToFileInfo();
var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds49to49.wav".ToFileInfo();
var output = @"C:\Ecoacoustics\SoftwareTests\TestOscillationSpectrogram".ToDirectoryInfo();
var expectedResultsDir = new DirectoryInfo(Path.Combine(output.FullName, TestTools.ExpectedResultsDir));
if (!expectedResultsDir.Exists)
Expand Down Expand Up @@ -101,7 +104,7 @@ public static void TESTMETHOD_DrawOscillationSpectrogram()
pathName = Path.Combine(output.FullName, fileName);
var csvFile1 = new FileInfo(pathName + ".csv");

fileName = sourceName + ".OSCSpectralIndex";
fileName = sourceName + ".SpectralIndex.OSC";
pathName = Path.Combine(output.FullName, fileName);
var csvFile2 = new FileInfo(pathName + ".csv");

Expand All @@ -124,8 +127,12 @@ public static void TESTMETHOD_GetSpectralIndex_Osc()
{
// 1. set up the resources
var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds30to32.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds45to46.wav".ToFileInfo();
//var sourceRecording = @"C:\Work\GitHub\audio-analysis\tests\Fixtures\Recordings\BAC2_20071008-085040_seconds49to49.wav".ToFileInfo();
var output = @"C:\Ecoacoustics\SoftwareTests\TestOscillationSpectrogram".ToDirectoryInfo();
var sourceName = Path.GetFileNameWithoutExtension(sourceRecording.Name);
var opStem = sourceName + ".SpectralIndex.OSC";
var expectedResultsDir = new DirectoryInfo(Path.Combine(output.FullName, TestTools.ExpectedResultsDir));
if (!expectedResultsDir.Exists)
{
Expand All @@ -135,17 +142,31 @@ public static void TESTMETHOD_GetSpectralIndex_Osc()
var configDict = GetDefaultConfigDictionary(sourceRecording);

// 2. Get the spectral index
var spectralIndex = GetSpectralIndex_Osc(sourceRecording, configDict);
var spectralIndexShort = GetSpectralIndex_Osc(sourceRecording, configDict);

// 3. Write the vector to csv file
var fileName1 = sourceName + ".OSCSpectralIndex.csv";
var pathName1 = new FileInfo(Path.Combine(output.FullName, fileName1));
// 3. double length of the vector because want to work with 256 element vector for LDFC purposes
var spectralIndex = DataTools.VectorDoubleLengthByAverageInterpolation(spectralIndexShort);

// 4. Write the vector to csv file
var pathName1 = new FileInfo(Path.Combine(output.FullName, opStem + ".csv"));
Acoustics.Shared.Csv.Csv.WriteToCsv(pathName1, spectralIndex);

// 4. draw image of the vector for debug purposes.
var vectorImage = ImageTools.DrawVectorInColour(DataTools.reverseArray(spectralIndex), cellWidth: 5);
var fileName2 = sourceName + ".SpectralIndex.OSC.png";
var pathName2 = Path.Combine(output.FullName, fileName2);
//var vectorImage = ImageTools.DrawVectorInColour(DataTools.reverseArray(spectralIndex), cellWidth: 5);
spectralIndex = DataTools.NormaliseByScalingMaxValueToOne(spectralIndex);
int cellWidth = 30;
int cellHeight = 2;
var vectorImage = ImageTools.DrawVectorInGrayScaleWithoutNormalisation(DataTools.reverseArray(spectralIndex), cellWidth, cellHeight);

// set up a frequency scale for easier interpretation
int herzInterval = 1000;
var sampleRate = double.Parse(configDict[AnalysisKeys.ResampleRate]);
var windowSize = double.Parse(configDict[AnalysisKeys.FrameLength]);
double freqBinWidth = sampleRate / windowSize / 2; // Divide by 2 bcause have doubled length of the spectral index vector
double yTicInterval = herzInterval / freqBinWidth * cellHeight;
int yOffset = cellHeight / 2;
vectorImage = ImageTools.DrawYaxisScale(vectorImage, 10, herzInterval, yTicInterval, yOffset);
var pathName2 = Path.Combine(output.FullName, opStem + ".png");
vectorImage.Save(pathName2, ImageFormat.Png);
}

Expand Down Expand Up @@ -209,7 +230,7 @@ public static Dictionary<string, string> GetConfigDictionary(FileInfo configFile
const int sampleLength = 128;
configDict[AnalysisKeys.OscilDetection2014SampleLength] = sampleLength.ToString();

const double sensitivityThreshold = 0.2;
const double sensitivityThreshold = 0.3;
configDict[AnalysisKeys.OscilDetection2014SensitivityThreshold] = sensitivityThreshold.ToString(CultureInfo.CurrentCulture);
return configDict;
}
Expand Down Expand Up @@ -268,6 +289,10 @@ public static Tuple<Image, double[,]> GenerateOscillationDataAndImages(FileInfo
sonogram.Data = MatrixTools.Submatrix(sonogram.Data, 0, 1, sonogram.FrameCount - 1, binCount - 1);
}

// get the appropriate sampleLength (patch size) for short recordings
int framecount = sonogram.Data.GetLength(0);
sampleLength = AdjustSampleSize(framecount, sampleLength);

var algorithmName1 = "autocorr-svd-fft";
var freqOscilMatrix1 = GetFrequencyByOscillationsMatrix(sonogram.Data, sensitivity, sampleLength, algorithmName1);
var image1 = GetFreqVsOscillationsImage(freqOscilMatrix1, sonogram.FramesPerSecond, sonogram.FBinWidth, sampleLength, algorithmName1);
Expand Down Expand Up @@ -352,6 +377,11 @@ public static Image GetFreqVsOscillationsImage(double[,] freqOscilMatrix, double
// each value is to be drawn as a 5 pixel x 5 pixel square
int xscale = 5;
int yscale = 5;
if (maxRows < 10)
{
xscale = 10;
}

var image1 = ImageTools.DrawMatrixInColour(freqOscilMatrix, xPixelsPerCell: xscale, yPixelsPerCell: yscale);

var image2 = ImageTools.DrawVectorInColour(DataTools.reverseArray(spectralIndex), cellWidth: xscale);
Expand Down Expand Up @@ -571,7 +601,7 @@ public static double[] GetOscillationArrayUsingSvdAndFft(double[,] xCorrByTimeMa
spectrum = DataTools.Subarray(spectrum, 1, spectrum.Length - 2);

// reduce the power in first coeff because it can dominate - this is a hack!
spectrum[0] *= 0.66;
spectrum[0] *= 0.5;

spectrum = DataTools.SquareValues(spectrum);

Expand Down Expand Up @@ -636,7 +666,7 @@ public static double[] GetOscillationArrayUsingFft(double[,] xCorrByTimeMatrix,

// reduce the power in the low coeff because these can dominate.
// This is a hack!
spectrum[0] *= 0.66;
spectrum[0] *= 0.33;

// convert to energy and calculate total power in spectrum
spectrum = DataTools.SquareValues(spectrum);
Expand Down Expand Up @@ -687,7 +717,7 @@ public static double[] GetOscillationArrayUsingWpd(double[,] xCorrByTimeMatrix,
double[] spectrum = wpd.GetWPDEnergySpectrumWithoutDC();

// reduce the power in first coeff because it can dominate - this is a hack!
spectrum[0] *= 0.66;
spectrum[0] *= 0.5;

spectrum = DataTools.SquareValues(spectrum);

Expand Down Expand Up @@ -830,16 +860,15 @@ public static double[] GetSpectralIndex_Osc(FileInfo sourceRecording, Dictionary
{
var sensitivity = double.Parse(configDict[AnalysisKeys.OscilDetection2014SensitivityThreshold]);

// Sample length i.e. number of frames spanned to calculate oscillations per second
int sampleLength = int.Parse(configDict[AnalysisKeys.OscilDetection2014SampleLength]);

// set up the default songram config object
var sonoConfig = new SonogramConfig(configDict)
{
WindowSize = int.Parse(configDict[AnalysisKeys.FrameLength]),
};

var recordingSegment = new AudioRecording(sourceRecording.FullName);

//double recordingLengthInSeconds = recordingSegment.Duration.TotalSeconds;
BaseSonogram sonogram = new AmplitudeSonogram(sonoConfig, recordingSegment.WavReader);

// Taking the square-root emphasizes the low amplitude features.
Expand All @@ -854,6 +883,14 @@ public static double[] GetSpectralIndex_Osc(FileInfo sourceRecording, Dictionary
sonogram.Data = MatrixTools.Submatrix(sonogram.Data, 0, 1, sonogram.FrameCount - 1, binCount - 1);
}

// Sample length i.e. number of frames spanned to calculate oscillations per second
int framecount = sonogram.Data.GetLength(0);

// get required sample length
int sampleLength = int.Parse(configDict[AnalysisKeys.OscilDetection2014SampleLength]);

// adjust sample length i.e. patch size for short recordings.
sampleLength = AdjustSampleSize(framecount, sampleLength);
var freqOscilMatrix = GetFrequencyByOscillationsMatrix(sonogram.Data, sensitivity, sampleLength, "autocorr-fft");

//NOTE: Generate an oscillations spectral index for making LDFC spectrograms by taking the max of each column
Expand Down Expand Up @@ -894,6 +931,34 @@ public static void GetOscillationUsingDct(double[] array, double framesPerSecond
intenisty = dctCoeff[indexOfMaxValue];
}

/// <summary>
/// Adjusts sample length i.e. patch size for short recordings
/// </summary>
/// <param name="framecount">number of frames in the frequency bin to be processed</param>
/// <param name="sampleLength">the number of frames to be included in each patch</param>
/// <returns>appropriately reduced patch size</returns>
public static int AdjustSampleSize(int framecount, int sampleLength)
{
if (framecount < sampleLength * 4)
{
sampleLength /= 2;
}

if (framecount < sampleLength * 2)
{
sampleLength = 32;
}

if (framecount < sampleLength * 2)
{
sampleLength = 8;
}

return sampleLength;
}



private static Image DrawTitleBarOfOscillationSpectrogram(string algorithmName, int width)
{
var longTitle = "Hz * Cycle/s (" + algorithmName + ")";
Expand Down
4 changes: 2 additions & 2 deletions src/AudioAnalysisTools/StandardSpectrograms/BaseSonogram.cs
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
// <copyright file="BaseSonogram.cs" company="QutEcoacoustics">
// <copyright file="BaseSonogram.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>

Expand Down Expand Up @@ -133,7 +133,7 @@ public BaseSonogram(SonogramConfig config, WavReader wav, bool dummy)
//bool doExtractSubband = this.SubBandMinHz > 0 || this.SubBandMaxHz < this.NyquistFrequency;

this.Duration = wav.Time;
double minDuration = 1.0;
double minDuration = 0.2;
if (this.Duration.TotalSeconds < minDuration)
{
LoggedConsole.WriteLine("Signal must at least {0} seconds long to produce a sonogram!", minDuration);
Expand Down
Loading

0 comments on commit 2eeeb44

Please sign in to comment.