Skip to content

Commit

Permalink
get the proportion of samples in each cluster
Browse files Browse the repository at this point in the history
  • Loading branch information
@mkholghi @atruskie
mkholghi authored and atruskie committed Jun 8, 2018
1 parent 7c5af4c commit d9ba1ae
Show file tree
Hide file tree
Showing 2 changed files with 87 additions and 37 deletions.
25 changes: 25 additions & 0 deletions src/AudioAnalysisTools/DSP/KmeansClustering.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@

namespace AudioAnalysisTools.DSP
{
using System.Diagnostics;
using System.IO;
using Accord.MachineLearning;
using Accord.Math;
using Accord.Math.Distances;
Expand All @@ -29,6 +31,29 @@ public static double[][] Clustering(double[,] patches, int noOfClust)
var clusters = kmeans.Learn(patches.ToJagged());
double[][] centroids = clusters.Centroids;

//get the cluster size
Dictionary<int, double> clusterIdSize = new Dictionary<int, double>();
for (int i = 0; i < clusters.Clusters.Length; i++)
{
//Compute the proportion of samples in the cluster
clusterIdSize.Add(clusters.Clusters[i].Index, clusters.Clusters[i].Proportion);
}

//sort clusters based on the number of samples
var items = from pair in clusterIdSize orderby pair.Value ascending select pair;

//writing to a csv file
using (StreamWriter file = new StreamWriter(@"C:\Users\kholghim\Mahnoosh\PcaWhitening\ClusterSize64.txt"))
{
foreach (var entry in items)
{
file.WriteLine("{0}\t{1}", entry.Key, entry.Value);
}
}
//string pathToCsv = @"C:\Users\kholghim\Mahnoosh\PcaWhitening\ClusterSize.csv";
//String csv = String.Join(Environment.NewLine, items.Select(d => d.Key + "\t" + d.Value + "\t"));
//System.IO.File.WriteAllText(pathToCsv, csv);

return centroids;
}
}
Expand Down
99 changes: 62 additions & 37 deletions tests/Acoustics.Test/AudioAnalysisTools/DSP/PcaWhiteningTest.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@ namespace Acoustics.Test.AudioAnalysisTools.DSP
using Microsoft.VisualStudio.TestTools.UnitTesting;
using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.Drawing;
using System.Drawing.Imaging;
using System.IO;
using System.Linq;
Expand All @@ -16,6 +18,7 @@ namespace Acoustics.Test.AudioAnalysisTools.DSP
using Accord.Statistics.Analysis;
using Accord.Math;
using Accord.Statistics.Kernels;
using Acoustics.Tools.Wav;
using global::AudioAnalysisTools.StandardSpectrograms;
using global::AudioAnalysisTools.WavTools;
using global::TowseyLibrary;
Expand Down Expand Up @@ -46,8 +49,8 @@ public void TestPcaWhitening()
{
var outputDir = this.outputDirectory;
var folderPath =
PathHelper.ResolveAssetPath("C:\\Users\\kholghim\\Mahnoosh\\PcaWhitening\\random_audio_segments\\1192");
var resultDir = PathHelper.ResolveAssetPath("C:\\Users\\kholghim\\Mahnoosh\\PcaWhitening");
PathHelper.ResolveAssetPath(@"C:\Users\kholghim\Mahnoosh\PcaWhitening\random_audio_segments\1192_1000");
var resultDir = PathHelper.ResolveAssetPath(@"C:\Users\kholghim\Mahnoosh\PcaWhitening");
//var resultDir = PathHelper.ResolveAssetPath("PcaWhitening");
var outputLinScaImagePath = Path.Combine(resultDir, "LinearFreqScaleSpectrogram.png");
var outputAmpSpecImagePath = Path.Combine(resultDir, "AmplitudeSpectrogram.png");
Expand Down Expand Up @@ -436,58 +439,73 @@ public void TestPcaWhitening()
List<double[,]> randomPatches = new List<double[,]>();
int patchWidth = finalBinCount; //256; //16; //full band patches
int patchHeight = 4; //16; // 2; // 4; // 6; //
int noOfRandomPatches = 50; //20; //10; //100; //500; //
int noOfRandomPatches = 10; //20; //10; //100; //500; //
//int fileCount = Directory.GetFiles(folderPath, "*.wav").Length;

foreach (string filePath in Directory.GetFiles(folderPath, "*.wav"))
{
FileInfo f = filePath.ToFileInfo();
if (f.Length == 0)
{
Debug.WriteLine(f.Name);
}
}

foreach (string filePath in Directory.GetFiles(folderPath, "*.wav"))
{
var recording = new AudioRecording(filePath);
sonoConfig.SourceFName = recording.BaseName;
FileInfo f = filePath.ToFileInfo();

var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
//process the wav file if it is not empty
if (f.Length != 0)
{
var recording = new AudioRecording(filePath);
sonoConfig.SourceFName = recording.BaseName;

var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);

// DO DRAW SPECTROGRAM
//var fst = freqScale.ScaleType;
//var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + freqScale.ScaleType.ToString(), freqScale.GridLineLocations);
//image.Save(outputImagePath, ImageFormat.Png);

// DO DRAW SPECTROGRAM
//var fst = freqScale.ScaleType;
//var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + freqScale.ScaleType.ToString(), freqScale.GridLineLocations);
//image.Save(outputImagePath, ImageFormat.Png);
//var image = amplitudeSpectrogram.GetImageFullyAnnotated(amplitudeSpectrogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//image.Save(outputLinScaImagePath, ImageFormat.Png);

//var image = amplitudeSpectrogram.GetImageFullyAnnotated(amplitudeSpectrogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//image.Save(outputLinScaImagePath, ImageFormat.Png);
// DO RMS NORMALIZATION
sonogram.Data = PcaWhitening.RmsNormalization(sonogram.Data);
//var normImage = amplitudeSpectrogram.GetImageFullyAnnotated(amplitudeSpectrogram.GetImage(), "NORMAmplitudeSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//normImage.Save(outputNormAmpImagePath, ImageFormat.Png);

// DO RMS NORMALIZATION
sonogram.Data = PcaWhitening.RmsNormalization(sonogram.Data);
//var normImage = amplitudeSpectrogram.GetImageFullyAnnotated(amplitudeSpectrogram.GetImage(), "NORMAmplitudeSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//normImage.Save(outputNormAmpImagePath, ImageFormat.Png);

// DO NOISE REDUCTION
/*
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
var noiseReducedImage = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "NOISEREDUCEDSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
noiseReducedImage.Save(outputNoiseReducedImagePath, ImageFormat.Png);
*/

// DO NOISE REDUCTION
/*
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
var noiseReducedImage = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "NOISEREDUCEDSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
noiseReducedImage.Save(outputNoiseReducedImagePath, ImageFormat.Png);
*/
//sonogram.Data = SNR.NoiseReduce_Median(sonogram.Data, nhBackgroundThreshold: 2.0);
sonogram.Data = PcaWhitening.NoiseReduction(sonogram.Data); //****

//sonogram.Data = SNR.NoiseReduce_Median(sonogram.Data, nhBackgroundThreshold: 2.0);
sonogram.Data = PcaWhitening.NoiseReduction(sonogram.Data); //****
//sonogram.Data = dataMatrix2;
//var noiseReducedImage = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "NOISEREDUCEDSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//noiseReducedImage.Save(outputNoiseReducedImagePath, ImageFormat.Png);

//sonogram.Data = dataMatrix2;
//var noiseReducedImage = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "NOISEREDUCEDSPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
//noiseReducedImage.Save(outputNoiseReducedImagePath, ImageFormat.Png);
// Do Patch Sampling
//int rows = sonogram.Data.GetLength(0); //3247
//int cols = sonogram.Data.GetLength(1); //256

// Do Patch Sampling
//int rows = sonogram.Data.GetLength(0); //3247
//int cols = sonogram.Data.GetLength(1); //256
randomPatches.Add(PatchSampling.GetPatches(sonogram.Data, patchWidth, patchHeight, noOfRandomPatches, "overlapped random").ToMatrix());
}

randomPatches.Add(PatchSampling.GetPatches(sonogram.Data, patchWidth, patchHeight, noOfRandomPatches, "overlapped random").ToMatrix());
}

//convert list of random patches matrices to one matrix
double[,] allPatchM = PatchSampling.ListOf2DArrayToOne2DArray(randomPatches);

//Do k-means clustering
int noOfClusters = 50;
int noOfClusters = 64; //10; // 50;
double[][] centroidMatrix = KmeansClustering.Clustering(allPatchM, noOfClusters);

List<double[,]> allCentroids = new List<double[,]>();
Expand All @@ -510,13 +528,20 @@ public void TestPcaWhitening()
double[,] mergedCentroidMatrix = PatchSampling.ListOf2DArrayToOne2DArray(allCentroids);

//Draw clusters
//var recording3 = new AudioRecording(Directory.GetFiles(folderPath, "*.wav")[0]);
//var sonogram3 = new SpectrogramStandard(sonoConfig, recording3.WavReader);
//sonogram3.Data = mergedCentroidMatrix;
//var clusterImage = sonogram3.GetImageFullyAnnotated(sonogram3.GetImage(), "ClusterCentroids: " + fst.ToString(), freqScale.GridLineLocations);
//int gridInterval = 1000;
//var freqScale = new FrequencyScale(FreqScaleType.Mel, nyquist, frameSize, finalBinCount, gridInterval);

var clusterImage = ImageTools.DrawMatrixWithoutNormalisation(mergedCentroidMatrix);
//clusterImage.RotateFlip(RotateFlipType.Rotate90FlipNone);
clusterImage.RotateFlip(RotateFlipType.Rotate270FlipNone);
clusterImage.Save(outputClusterImagePath, ImageFormat.Bmp);

//string filename = @"C:\Users\kholghim\Mahnoosh\PcaWhitening\Clusters50.bmp";
string outputFile = @"C:\Users\kholghim\Mahnoosh\PcaWhitening\Clusters64WithGrid.bmp";
//Image bmp = ImageTools.ReadImage2Bitmap(filename);
FrequencyScale.DrawFrequencyLinesOnImage((Bitmap)clusterImage, freqScale, includeLabels: false);
clusterImage.Save(outputFile);

var actual = PcaWhitening.Whitening(allPatchM);

//Processing the target spectrogram
Expand Down

0 comments on commit d9ba1ae

Please sign in to comment.