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extended the drawing method to highlight bands bounadries
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@mkholghi @atruskie
mkholghi authored and atruskie committed Feb 4, 2019
1 parent e3577e1 commit 470283d
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Showing 3 changed files with 89 additions and 15 deletions.
4 changes: 2 additions & 2 deletions src/AnalysisPrograms/SpectralPeakTracking/SpectralPeakTrackingEntry.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -86,10 +86,10 @@ public static void Execute(Arguments arguments)

// Noise Reduction to be added

var localPeaks = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.Settings, hertzPerFreqBin);
var localPeaksBands = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.Settings, hertzPerFreqBin);

// draw the local peaks
double[,] hits = SpectralPeakTracking2018.MakeHitMatrix(energySpectrogram.Data, localPeaks);
double[,] hits = SpectralPeakTracking2018.MakeHitMatrix(energySpectrogram.Data, localPeaksBands.Item1, localPeaksBands.Item2);
var image = SpectralPeakTracking2018.DrawSonogram(energySpectrogram, hits);
image.Save(imagePath, ImageFormat.Bmp);
}
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88 changes: 79 additions & 9 deletions src/AudioAnalysisTools/SpectralPeakTracking2018.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ namespace AudioAnalysisTools
using System;
using System.Collections.Generic;
using System.Drawing;
using System.Linq;
using StandardSpectrograms;
using TowseyLibrary;

Expand All @@ -15,7 +16,7 @@ namespace AudioAnalysisTools
/// </summary>
public static class SpectralPeakTracking2018
{
public static int[][] SpectralPeakTracking(double[,] spectrogram, SpectralPeakTrackingSettings settings, double hertzPerFreqBin)
public static Tuple<int[][], int[][]> SpectralPeakTracking(double[,] spectrogram, SpectralPeakTrackingSettings settings, double hertzPerFreqBin)
{
if (spectrogram == null)
{
Expand All @@ -33,12 +34,19 @@ public static int[][] SpectralPeakTracking(double[,] spectrogram, SpectralPeakTr
var bottomSideBinWidth = Convert.ToInt32(settings.BottomSideBand / hertzPerFreqBin);

// find the local peak per spectrum
int[][] localPeaks = FindLocalSpectralPeaks(spectrogram, peakBinsIndex, syllableBinWidth, topSideBinWidth, bottomSideBinWidth, settings.DbThreshold);
Tuple<int[][], int[][]> localPeaksAndBands = FindLocalSpectralPeaks(spectrogram, peakBinsIndex, syllableBinWidth, topSideBinWidth, bottomSideBinWidth, settings.DbThreshold);

return localPeaks;
// make an array of zero and one local peaks
int[] SpectralPeakArray = MakeSpectralPeakArray(spectrogram, localPeaksAndBands.Item1);

double frameDuration = 1024 / 48000;
double framesPerSecond = 60 / frameDuration;
int herzOffset = 0;

// Do Spectral Peak Tracking
// SpectralTrack.GetSpectralPeakTracks()
var spectralTracks = SpectralTrack.GetSpectralTracks(SpectralPeakArray, framesPerSecond, hertzPerFreqBin, herzOffset, SpectralTrack.MIN_TRACK_DURATION, SpectralTrack.MAX_INTRASYLLABLE_GAP, SpectralTrack.MAX_FREQ_BOUND);

return localPeaksAndBands;
}

/// <summary>
Expand All @@ -61,20 +69,26 @@ public static int[] GetPeakBinsIndex(double[,] matrix, int minFreqBin, int maxFr
return peakBins;
}

public static int[][] FindLocalSpectralPeaks(double[,] matrix, int[] peakBinsIndex, int widthMidBand,
public static Tuple<int[][], int[][]> FindLocalSpectralPeaks(double[,] matrix, int[] peakBinsIndex, int widthMidBand,
int topBufferSize, int bottomBufferSize, double threshold)
{
int frameCount = matrix.GetLength(0);

// save the target peak bins index [frameCount, freqBinCount]
List<int[]> targetPeakBinsIndex = new List<int[]>();

// save the bands' boundaries in each frame
List<int[]> bandIndex = new List<int[]>();

// for all frames of the input spectrogram
for (int r = 0; r < frameCount; r++)
{
// retrieve each frame
double[] spectrum = DataTools.GetRow(matrix, r);

// smoothing to remove noise
spectrum = DataTools.filterMovingAverage(spectrum, 3);

//find the boundaries of middle frequency band: the min bin index and the max bin index
int minMid = peakBinsIndex[r] - (widthMidBand / 2);
int maxMid = peakBinsIndex[r] + (widthMidBand / 2);
Expand All @@ -100,6 +114,7 @@ public static int[][] FindLocalSpectralPeaks(double[,] matrix, int[] peakBinsInd
double peakEnergy = midBandAvgEnergy - ((topBandAvgEnergy + bottomBandAvgEnergy) / 2);

int[] ind = new int[2];
int[] bandInd = new int[5];

// convert avg enerrgy to decibel values
var peakEnergyInDb = 10 * Math.Log10(peakEnergy);
Expand All @@ -111,9 +126,17 @@ public static int[][] FindLocalSpectralPeaks(double[,] matrix, int[] peakBinsInd
ind[1] = peakBinsIndex[r];
targetPeakBinsIndex.Add(ind);
}

// saving the index of top, mid, and bottom band boundaries
bandInd[0] = r;
bandInd[1] = minBottom;
bandInd[2] = minMid;
bandInd[3] = maxMid;
bandInd[4] = maxTop;
bandIndex.Add(bandInd);
}

return targetPeakBinsIndex.ToArray();
return Tuple.Create(targetPeakBinsIndex.ToArray(), bandIndex.ToArray());
}

/// <summary>
Expand Down Expand Up @@ -156,20 +179,67 @@ public static double CalculateAverageEnergy(double[] spectrum, int minInd, int m
return outputMatrix;
}

public static double[,] MakeHitMatrix(double[,] matrix, int[][] pointsOfInterest)
/// <summary>
/// outputs a matrix with the same size of the input matrix.
/// all values are zero, except the points of interest (i.e., local spectral peaks).
/// these bins can be filled with amplitude values or 1.
/// </summary>
public static double[,] MakeHitMatrix(double[,] matrix, int[][] pointsOfInterest, int[][] bandIndex)
{
// initialize a matrix with the same size of the input matrix with zero values
double[,] hits = new double[matrix.GetLength(0), matrix.GetLength(1)];

for (int i = 0; i < pointsOfInterest.GetLength(0); i++)
{
int rowIndex = pointsOfInterest[i][0];
int colIndex = pointsOfInterest[i][1];
hits[rowIndex, colIndex] = 1.0;
hits[rowIndex, colIndex] = 1.0; // matrix[rowIndex, colIndex]

/*
// bands
int colIndex1 = bandIndex[i][1];
int colIndex2 = bandIndex[i][2];
int colIndex3 = bandIndex[i][3];
int colIndex4 = bandIndex[i][4];
hits[rowIndex, colIndex1] = 1.0;
hits[rowIndex, colIndex2] = 1.0;
hits[rowIndex, colIndex3] = 1.0;
hits[rowIndex, colIndex4] = 1.0;
*/
}

// bands
for (int i = 0; i < bandIndex.GetLength(0); i++)
{
int rowIndex = bandIndex[i][0];
int colIndex1 = bandIndex[i][1];
int colIndex2 = bandIndex[i][2];
int colIndex3 = bandIndex[i][3];
int colIndex4 = bandIndex[i][4];
hits[rowIndex, colIndex1] = 1.0;
hits[rowIndex, colIndex2] = 1.0;
hits[rowIndex, colIndex3] = 1.0;
hits[rowIndex, colIndex4] = 1.0;
}

return hits;
}

public static int[] MakeSpectralPeakArray(double[,] matrix, int[][] targetPeakBinsIndex)
{
int[] peakArray = new int[matrix.GetLength(0)];
for (int i = 0; i < targetPeakBinsIndex.GetLength(0); i++)
{
int ind = targetPeakBinsIndex[i][0];
peakArray[ind] = targetPeakBinsIndex[i][1];
}

return peakArray;
}

/// <summary>
/// draw the spectrogram with red marks indicating the local spectral peaks.
/// </summary>
public static Image DrawSonogram(BaseSonogram sonogram, double[,] hits)
{
Image_MultiTrack image = new Image_MultiTrack(sonogram.GetImage());
Expand All @@ -192,7 +262,7 @@ public class SpectralPeakTrackingSettings
public const int DefaultMaxSearchFreq = 3500;

// width of the middle frequency search band in Hertz.
public const int DefaultSyllableBandWidth = 1000;
public const int DefaultSyllableBandWidth = 500;

// a bottom and top buffer band in Hertz
public const int DefaultBottomSideBand = 500;
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12 changes: 8 additions & 4 deletions tests/Acoustics.Test/AudioAnalysisTools/SpectralPeakTracking2018Tests.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ public void FindLocalSpectralPeaksTest()
double threshold = 4.0;

var actualLocalPeaks = SpectralPeakTracking2018.FindLocalSpectralPeaks(matrix, peakBinsIndex, widthMidBand,
topBufferSize, bottomBufferSize, threshold);
topBufferSize, bottomBufferSize, threshold).Item1;

for (int i = 0; i < expectedLocalPeaksIndex.GetLength(0); i++)
{
Expand All @@ -70,7 +70,7 @@ public void FindLocalSpectralPeaksTest()

[Ignore]
[TestMethod]
public void SpectralPeakTest()
public void LocalSpectralPeakTest()
{
var configPath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\SpectralPeakTrackingConfig.yml";
var recordingPath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\JY-(cleaned)-3-Night_Parrot-pair.Western_Qld.wav";
Expand Down Expand Up @@ -112,14 +112,18 @@ public void SpectralPeakTest()
var amplitudeSpectrogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
var energySpectrogram = new EnergySpectrogram(amplitudeSpectrogram);
var decibelSpectrogram = new SpectrogramStandard(sonoConfig, recording.WavReader);

// Noise Reduction to be added

var localPeaks = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.Settings, hertzPerFreqBin);
var localPeaksBands = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.Settings, hertzPerFreqBin);

// draw the local peaks
double[,] hits = SpectralPeakTracking2018.MakeHitMatrix(energySpectrogram.Data, localPeaks);
double[,] hits = SpectralPeakTracking2018.MakeHitMatrix(energySpectrogram.Data, localPeaksBands.Item1, localPeaksBands.Item2);
var image = SpectralPeakTracking2018.DrawSonogram(decibelSpectrogram, hits);
image.Save(imagePath, ImageFormat.Bmp);

// make an array of zero and one local peaks
//int[] SpectralPeakArray = SpectralPeakTracking2018.MakeSpectralPeakArray(energySpectrogram.Data, localPeaksBands.Item1);
}
}
}

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