Skip to content

Commit

Permalink
fixed bugs in new peak tracking method
Browse files Browse the repository at this point in the history
  • Loading branch information
@mkholghi @atruskie
mkholghi authored and atruskie committed Feb 4, 2019
1 parent 2af60bf commit 29af151
Show file tree
Hide file tree
Showing 2 changed files with 78 additions and 34 deletions.
67 changes: 43 additions & 24 deletions src/AudioAnalysisTools/SpectralPeakTracking2018.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ namespace AudioAnalysisTools
using System.Collections.Generic;
using System.Drawing;
using System.IO;
using System.Linq;
using Accord.Statistics.Kernels;
using Acoustics.Shared.Csv;
using StandardSpectrograms;
Expand All @@ -24,7 +25,7 @@ public class Output

public int[][] BandIndex { get; set; }

public object[][] peakTrackInfoList { get; set; }
public List<object[]> peakTrackInfoList { get; set; }

//public List<SpectralTrack> SpecTracks { get; set; }
}
Expand Down Expand Up @@ -52,6 +53,7 @@ public static Output SpectralPeakTracking(double[,] spectrogram, SpectralPeakTra
// make an array of the index of local peaks. Zero means there is no local peak identified.
int[] SpectralPeakArray = MakeSpectralPeakArray(spectrogram, localPeaksAndBands.Item1);

// find a track of peaks in a pre-defined set of boundaries
var peakTrackInfo = SpectralPeakTracking(spectrogram, SpectralPeakArray, timePerFrame, hertzPerFreqBin);

/*
Expand Down Expand Up @@ -168,18 +170,19 @@ public static Tuple<int[][], int[][]> FindLocalSpectralPeaks(double[,] matrix, i
return Tuple.Create(targetPeakBinsIndex.ToArray(), bandIndex.ToArray());
}

public static object[][] SpectralPeakTracking(double[,] spectrogram, int[] SpectralPeakArray, double timePerFrame, double hertzPerFreqBin)
public static List<object[]> SpectralPeakTracking(double[,] spectrogram, int[] SpectralPeakArray, double timePerFrame, double hertzPerFreqBin)
{
int startX;
int endX;
int startY;
int endY;
int peakCount = 0;
var score = 0;

List<object[]> peakTrackInfoList = new List<object[]>();

for (int i = 0; i < SpectralPeakArray.Length; i++)
{
int peakCount = 0;
var score = 0;
if (SpectralPeakArray[i] != 0)
{
object[] peakTrackInfo = new object[6];
Expand All @@ -188,36 +191,52 @@ public static object[][] SpectralPeakTracking(double[,] spectrogram, int[] Spect
endX = startX + 17;
endY = startY + 4;
//double[,] targetMatrix = GetArbitraryMatrix(spectrogram, startY, endY, startX, endX);
for (int j = startX; j < endX; j++)

if (endX < spectrogram.GetLength(0) && endY < spectrogram.GetLength(1))
{
if (SpectralPeakArray[j] >= startY && SpectralPeakArray[j] <= endY)
for (int j = startX; j < endX; j++)
{
peakCount++;
if (SpectralPeakArray[j] >= startY && SpectralPeakArray[j] <= endY)
{
peakCount++;
}
}
}

score = peakCount / 18;
score = peakCount; //peakCount / 18;

peakTrackInfo[0] = i; // frame number
peakTrackInfo[1] = i * timePerFrame;
peakTrackInfo[2] = SpectralPeakArray[i]; // bin number
peakTrackInfo[3] = SpectralPeakArray[i] * hertzPerFreqBin;
peakTrackInfo[4] = score;
if (score >= 5) //4 / 18
{
peakTrackInfo[0] = i; // frame number
peakTrackInfo[1] = i * timePerFrame;
peakTrackInfo[2] = SpectralPeakArray[i]; // bin number
peakTrackInfo[3] = SpectralPeakArray[i] * hertzPerFreqBin;
peakTrackInfo[4] = score;
peakTrackInfo[5] = "Yes";
peakTrackInfoList.Add(peakTrackInfo);
}

if (score >= 4 / 18)
{
peakTrackInfo[5] = "Yes";
}
else
{
peakTrackInfo[5] = "No";
}
/*
peakTrackInfo[0] = i; // frame number
peakTrackInfo[1] = i * timePerFrame;
peakTrackInfo[2] = SpectralPeakArray[i]; // bin number
peakTrackInfo[3] = SpectralPeakArray[i] * hertzPerFreqBin;
peakTrackInfo[4] = score;
peakTrackInfoList.Add(peakTrackInfo);
if (score >= 4) //4 / 18
{
peakTrackInfo[5] = "Yes";
}
else
{
peakTrackInfo[5] = "No";
}
peakTrackInfoList.Add(peakTrackInfo);
*/
}
}
}

return peakTrackInfoList.ToArray();
return peakTrackInfoList;

}

Expand Down
45 changes: 35 additions & 10 deletions tests/Acoustics.Test/AudioAnalysisTools/SpectralPeakTracking2018Tests.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,11 @@
namespace Acoustics.Test.AudioAnalysisTools
{
using System;
using System.Collections.Generic;
using System.Drawing.Imaging;
using System.IO;
using System.Linq;
using System.Text;
using Acoustics.Shared;
using Acoustics.Shared.ConfigFile;
using Acoustics.Shared.Csv;
Expand Down Expand Up @@ -56,7 +59,7 @@ public void FindLocalSpectralPeaksTest()
int widthMidBand = 4;
int topBufferSize = 2;
int bottomBufferSize = 2;
double threshold = 4.0;
double threshold = 1.0;

var actualLocalPeaks = SpectralPeakTracking2018.FindLocalSpectralPeaks(matrix, peakBinsIndex, widthMidBand,
topBufferSize, bottomBufferSize, threshold).Item1;
Expand All @@ -73,10 +76,10 @@ public void FindLocalSpectralPeaksTest()
public void LocalSpectralPeakTest()
{
var configPath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\SpectralPeakTrackingConfig.yml";
var recordingPath = @"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM7 24 Sep 2018 5.30 am.wav";// "Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM27 22 Sep 2018 3.30 am.wav"; //"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM16 24 Sep 2018 6.30 am.wav"; //"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM16 23 Sep 2018 6.30 am.wav"; //"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM7 24 Sep 2018 6.30 am.wav"; //"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM7 24 Sep 2018 5.30 am.wav";// "Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM4 24 Sep 2018 6.30 am.wav"; //"C:\Users\kholghim\Mahnoosh\Night_parrot\Night Parrot call-WA-hollow whistle-didit.wav";//"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM3 24 Sep 2018 6.30 am.wav"; //"C:\Users\kholghim\Mahnoosh\Night_parrot\JY-(cleaned)-3-Night_Parrot-pair.Western_Qld_downsampled.wav"; //"C:\Users\kholghim\Mahnoosh\Night_parrot\SM16 24 Sep 2018 6.30 am.wav"; //"C:\Users\kholghim\Mahnoosh\Night_parrot\S4A07296_20180419_050023_11-12min.wav"; //"M:\Postdoc\Night_parrot\S4A07296_20180419_050023_Ch1.wav"; //
var imagePath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\image_whistle_peaks_SM7 24 Sep 2018 5.30 am_1500_3500_100_250_3.bmp"; //image_NP_SM16 24 Sep 2018 6.30 am.bmp";
var recordingPath = @"Y:\RichardSeaton\NP Monitoring\Kalamurina May18\Night Parrot calls Kala 2018\SM27 22 Sep 2018 3.30 am.wav";
var imagePath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\image_whistle_peaks_SM27 22 Sep 2018 3.30 am_1500_3500_100_250_6.bmp";
//var trackImagePath = @"C:\Users\kholghim\Mahnoosh\Night_parrot\trackImage.bmp";
var pathToCsvFile = @"C:\Users\kholghim\Mahnoosh\Night_parrot\PeakTrackInfo.csv";
var pathToCsvFile = @"C:\Users\kholghim\Mahnoosh\Night_parrot\PeakTrackInfo_SM27 22 Sep 2018 3.30 am.csv";

var configFile = configPath.ToFileInfo();

Expand Down Expand Up @@ -110,26 +113,48 @@ public void LocalSpectralPeakTest()
NoiseReductionType = NoiseReductionType.None,
};

var frameStep = frameSize - (frameSize / frameOverlap);
var secondsPerFrame = frameSize / (nyquist * 2);
var timePerFrame = frameStep * secondsPerFrame;
var frameStep = frameSize * (1 - frameOverlap);
var secondsPerFrame = frameStep / (nyquist * 2);

//var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
var amplitudeSpectrogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
var energySpectrogram = new EnergySpectrogram(amplitudeSpectrogram);
var decibelSpectrogram = new SpectrogramStandard(sonoConfig, recording.WavReader);

// Noise Reduction to be added
// Noise Reduction
//var noiseReducedSpectrogram = SNR.NoiseReduce_Standard(energySpectrogram.Data);

var output = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.SptSettings, hertzPerFreqBin, timePerFrame);
var output = SpectralPeakTracking2018.SpectralPeakTracking(energySpectrogram.Data, configuration.SptSettings, hertzPerFreqBin, secondsPerFrame);

// draw the local peaks
double[,] hits = SpectralPeakTracking2018.MakeHitMatrix(energySpectrogram.Data, output.TargetPeakBinsIndex, output.BandIndex);
var image = SpectralPeakTracking2018.DrawSonogram(decibelSpectrogram, hits);
image.Save(imagePath, ImageFormat.Bmp);

Csv.WriteToCsv(pathToCsvFile.ToFileInfo(), output.peakTrackInfoList);
string[] header = new[] { "Frame No", "Start Time", "Bin No", "Freq", "Score", "Detection" };
var csv = new StringBuilder();
string content = string.Empty;
foreach (var entry in header.ToArray())
{
content += entry.ToString() + ",";
}

csv.AppendLine(content);

foreach (var entry in output.peakTrackInfoList)
{
content = string.Empty;
foreach (var value in entry)
{
content += value.ToString() + ",";
}

csv.AppendLine(content);
}

File.WriteAllText(pathToCsvFile, csv.ToString());

//Csv.WriteMatrixToCsv(pathToCsvFile.ToFileInfo(), output.peakTrackInfoList);

// draw spectral tracks
//var trackImage = SpectralPeakTracking2018.DrawTracks(decibelSpectrogram, hits, output.SpecTracks);
Expand Down

0 comments on commit 29af151

Please sign in to comment.