// #############################################################################################################################
// ################################# FOUR DIFFERENT METHODS TO CALCULATE THE BACKGROUND NOISE PROFILE
//
// (1) MODAL METHOD
// (2) LOWEST PERCENTILE FRAMES METHOD
// (3) BIN-WISE LOWEST PERCENTILE CELLS METHOD
// (4) FIRST N FRAMES
// ##################
/// <summary>
/// (1) MODAL METHOD
/// Assumes the passed matrix is a spectrogram. i.e. rows=frames, cols=freq bins.
/// Returns the noise profile over freq bins. i.e. one noise value per freq bin.
/// </summary>
/// <param name="matrix">the spectrogram with origin top-left</param>
/// <param name="sdCount">number of standard deviations</param>
public static NoiseProfile CalculateModalNoiseProfile(double[,] matrix, double sdCount)
{
int colCount = matrix.GetLength(1);
double[] noiseMode = new double[colCount];
double[] noiseSd = new double[colCount];
double[] noiseThreshold = new double[colCount];
double[] minsOfBins = new double[colCount];
double[] maxsOfBins = new double[colCount];
for (int col = 0; col < colCount; col++)
{
double[] freqBin = MatrixTools.GetColumn(matrix, col);
SNR.BackgroundNoise binNoise = SNR.CalculateModalBackgroundNoiseInSignal(freqBin, sdCount);
noiseMode[col] = binNoise.NoiseMode;
noiseSd[col] = binNoise.NoiseSd;
noiseThreshold[col] = binNoise.NoiseThreshold;
minsOfBins[col] = binNoise.MinDb;
maxsOfBins[col] = binNoise.MaxDb;
}
var profile = new NoiseProfile()
{
NoiseMode = noiseMode,
NoiseSd = noiseSd,
NoiseThresholds = noiseThreshold,
MinDb = minsOfBins,
MaxDb = maxsOfBins,
};
return(profile);
}
/// <summary>
/// Calls the algorithm of Lamel et al, 1981.
/// IMPORTANT: The passed signal envelope values are absolute amplitude values derived from the framed waveform.
/// These are converted to decibels before passing to the LAMEL method.
/// NOTE: The returned background noise value ignores the SD part of the Gaussian noise model.
/// </summary>
/// <param name="signalEnvelope">Amplitude values</param>
/// <returns>Modal noise value in decibels</returns>
public static double CalculateBackgroundNoise(double[] signalEnvelope)
{
var dBarray = SNR.Signal2Decibels(signalEnvelope);
CalculateNoiseUsingLamelsAlgorithm(dBarray, out double _, out double _, out double noiseMode, out double _);
return(noiseMode);
}
//##################################################################################################################################
/// <summary>
/// NOTE!!!! The decibel array has been normalised in 0 - 1.
/// </summary>
protected static Tuple <double[, ], double[]> MakeCepstrogram(SonogramConfig config, double[,] matrix, double[] decibels, int sampleRate)
{
double[,] m = matrix;
int nyquist = sampleRate / 2;
double epsilon = config.epsilon;
bool includeDelta = config.mfccConfig.IncludeDelta;
bool includeDoubleDelta = config.mfccConfig.IncludeDoubleDelta;
//Log.WriteIfVerbose(" MakeCepstrogram(matrix, decibels, includeDelta=" + includeDelta + ", includeDoubleDelta=" + includeDoubleDelta + ")");
//(i) APPLY FILTER BANK
int bandCount = config.mfccConfig.FilterbankCount;
bool doMelScale = config.mfccConfig.DoMelScale;
int ccCount = config.mfccConfig.CcCount;
int fftBinCount = config.FreqBinCount; //number of Hz bands = 2^N +1. Subtract DC bin
int minHz = config.MinFreqBand ?? 0;
int maxHz = config.MaxFreqBand ?? nyquist;
Log.WriteIfVerbose("ApplyFilterBank(): Dim prior to filter bank =" + matrix.GetLength(1));
//error check that filterBankCount < FFTbins
if (bandCount > fftBinCount)
{
throw new Exception(
"## FATAL ERROR in BaseSonogram.MakeCepstrogram():- Can't calculate cepstral coeff. FilterbankCount > FFTbins. (" +
bandCount + " > " + fftBinCount + ")\n\n");
}
//this is the filter count for full bandwidth 0-Nyquist. This number is trimmed proportionately to fit the required bandwidth.
if (doMelScale)
{
m = MFCCStuff.MelFilterBank(m, bandCount, nyquist, minHz, maxHz); // using the Greg integral
}
else
{
m = MFCCStuff.LinearFilterBank(m, bandCount, nyquist, minHz, maxHz);
}
Log.WriteIfVerbose("\tDim after filter bank=" + m.GetLength(1) + " (Max filter bank=" + bandCount + ")");
//(ii) CONVERT AMPLITUDES TO DECIBELS
m = MFCCStuff.DecibelSpectra(m, config.WindowPower, sampleRate, epsilon); //from spectrogram
//(iii) NOISE REDUCTION
var tuple1 = SNR.NoiseReduce(m, config.NoiseReductionType, config.NoiseReductionParameter);
m = tuple1.Item1;
//(iv) calculate cepstral coefficients
m = MFCCStuff.Cepstra(m, ccCount);
//(v) NormaliseMatrixValues
m = DataTools.normalise(m);
//(vi) Calculate the full range of MFCC coefficients ie including decibel and deltas, etc
m = MFCCStuff.AcousticVectors(m, decibels, includeDelta, includeDoubleDelta);
var tuple2 = Tuple.Create(m, tuple1.Item2);
return(tuple2); // return matrix and full bandwidth modal noise profile
}
public void LinearFrequencyScale()
{
var recordingPath = PathHelper.ResolveAsset("Recordings", "BAC2_20071008-085040.wav");
var opFileStem = "BAC2_20071008";
var outputDir = this.outputDirectory;
var outputImagePath = Path.Combine(outputDir.FullName, "LinearScaleSonogram.png");
var recording = new AudioRecording(recordingPath);
// specfied linear scale
int nyquist = 11025;
int frameSize = 1024;
int hertzInterval = 1000;
var freqScale = new FrequencyScale(nyquist, frameSize, hertzInterval);
var fst = freqScale.ScaleType;
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
sonogram.Configuration.WindowSize = freqScale.WindowSize;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
image.Save(outputImagePath, ImageFormat.Png);
// DO FILE EQUALITY TEST
var stemOfExpectedFile = opFileStem + "_LinearScaleGridLineLocations.EXPECTED.json";
var stemOfActualFile = opFileStem + "_LinearScaleGridLineLocations.ACTUAL.json";
// Check that freqScale.GridLineLocations are correct
var expectedFile1 = PathHelper.ResolveAsset("FrequencyScale\\" + stemOfExpectedFile);
if (!expectedFile1.Exists)
{
LoggedConsole.WriteErrorLine("An EXPECTED results file does not exist. Test will fail!");
LoggedConsole.WriteErrorLine(
$"If ACTUAL results file is correct, move it to dir `{PathHelper.TestResources}` and change its suffix to <.EXPECTED.json>");
}
var resultFile1 = new FileInfo(Path.Combine(outputDir.FullName, stemOfActualFile));
Json.Serialise(resultFile1, freqScale.GridLineLocations);
FileEqualityHelpers.TextFileEqual(expectedFile1, resultFile1);
// Check that image dimensions are correct
Assert.AreEqual(566, image.Height);
Assert.AreEqual(1621, image.Width);
}
/// <summary>
/// This method takes an audio recording and returns an octave scale spectrogram.
/// At the present time it only works for recordings with 64000 sample rate and returns a 256 bin sonogram.
/// TODO: generalise this method for other recordings and octave scales.
/// </summary>
public static BaseSonogram ConvertRecordingToOctaveScaleSonogram(AudioRecording recording, FreqScaleType fst)
{
var freqScale = new FrequencyScale(fst);
double windowOverlap = 0.75;
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.WindowSize,
WindowOverlap = windowOverlap,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
// Generate amplitude sonogram and then conver to octave scale
var sonogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
// THIS IS THE CRITICAL LINE.
// TODO: SHOULD DEVELOP A SEPARATE UNIT TEST for this method
sonogram.Data = ConvertAmplitudeSpectrogramToDecibelOctaveScale(sonogram.Data, freqScale);
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
int windowSize = freqScale.FinalBinCount * 2;
sonogram.Configuration.WindowSize = windowSize;
sonogram.Configuration.WindowStep = (int)Math.Round(windowSize * (1 - windowOverlap));
return(sonogram);
}
/// <summary>
/// Use this method when want to match defined shape in target using cross-correlation.
/// This was the method used by Stewart Gage.
/// First set target and source to same dynamic range.
/// Then NormaliseMatrixValues target and source to unit-length.
/// </summary>
public static Tuple <double[]> Execute_StewartGage(double[,] target, double dynamicRange, SpectrogramStandard sonogram,
List <AcousticEvent> segments, int minHz, int maxHz, double minDuration)
{
Log.WriteLine("SEARCHING FOR EVENTS LIKE TARGET.");
if (segments == null)
{
return(null);
}
int minBin = (int)(minHz / sonogram.FBinWidth);
int maxBin = (int)(maxHz / sonogram.FBinWidth);
int targetLength = target.GetLength(0);
//adjust target's dynamic range to that set by user
target = SNR.SetDynamicRange(target, 0.0, dynamicRange); //set event's dynamic range
double[] v1 = DataTools.Matrix2Array(target);
v1 = DataTools.normalise2UnitLength(v1);
//var image = BaseSonogram.Data2ImageData(target);
//ImageTools.DrawMatrix(image, 1, 1, @"C:\SensorNetworks\Output\FELT_Currawong\target.png");
double[] scores = new double[sonogram.FrameCount];
foreach (AcousticEvent av in segments)
{
Log.WriteLine("SEARCHING SEGMENT.");
int startRow = (int)Math.Round(av.TimeStart * sonogram.FramesPerSecond);
int endRow = (int)Math.Round(av.TimeEnd * sonogram.FramesPerSecond);
if (endRow >= sonogram.FrameCount)
{
endRow = sonogram.FrameCount;
}
int stopRow = endRow - targetLength;
if (stopRow <= startRow)
{
stopRow = startRow + 1; //want minimum of one row
}
int offset = targetLength / 2;
for (int r = startRow; r < stopRow; r++)
{
double[,] matrix = DataTools.Submatrix(sonogram.Data, r, minBin, r + targetLength - 1, maxBin);
matrix = SNR.SetDynamicRange(matrix, 0.0, dynamicRange); //set event's dynamic range
//var image = BaseSonogram.Data2ImageData(matrix);
//ImageTools.DrawMatrix(image, 1, 1, @"C:\SensorNetworks\Output\FELT_CURLEW\compare.png");
double[] v2 = DataTools.Matrix2Array(matrix);
v2 = DataTools.normalise2UnitLength(v2);
scores[r] = DataTools.DotProduct(v1, v2); //the Cross Correlation
} // end of rows in segment
} // foreach (AcousticEvent av in segments)
var tuple = Tuple.Create(scores);
return(tuple);
}
public void LinearFrequencyScaleDefault()
{
// relative path because post-Build command transfers files to ...\\Work\GitHub\...\bin\Debug subfolder.
var recordingPath = @"Recordings\BAC2_20071008-085040.wav";
var opFileStem = "BAC2_20071008";
var outputDir = this.outputDirectory;
var outputImagePath = Path.Combine(outputDir.FullName, "DefaultLinearScaleSonogram.png");
var recording = new AudioRecording(recordingPath);
// default linear scale
var fst = FreqScaleType.Linear;
var freqScale = new FrequencyScale(fst);
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
sonogram.Configuration.WindowSize = freqScale.WindowSize;
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
image.Save(outputImagePath, ImageFormat.Png);
// DO UNIT TESTING
var stemOfExpectedFile = opFileStem + "_DefaultLinearScaleGridLineLocations.EXPECTED.json";
var stemOfActualFile = opFileStem + "_DefaultLinearScaleGridLineLocations.ACTUAL.json";
// Check that freqScale.GridLineLocations are correct
var expectedFile1 = new FileInfo("FrequencyScale\\" + stemOfExpectedFile);
if (!expectedFile1.Exists)
{
LoggedConsole.WriteErrorLine("An EXPECTED results file does not exist. Test will fail!");
LoggedConsole.WriteErrorLine("If ACTUAL results file is correct, move it to dir <...\\TestResources\\FrequencyScale> and change its suffix to <.EXPECTED.json>");
}
var resultFile1 = new FileInfo(Path.Combine(outputDir.FullName, stemOfActualFile));
Json.Serialise(resultFile1, freqScale.GridLineLocations);
FileEqualityHelpers.TextFileEqual(expectedFile1, resultFile1);
// Check that image dimensions are correct
Assert.AreEqual(310, image.Height);
Assert.AreEqual(3247, image.Width);
}
public void LinearFrequencyScale()
{
var recordingPath = PathHelper.ResolveAsset("Recordings", "BAC2_20071008-085040.wav");
var outputImagePath = this.outputDirectory.CombineFile("DefaultLinearScaleSonogram.png");
var recording = new AudioRecording(recordingPath);
// specfied linear scale
int nyquist = 11025;
int frameSize = 1024;
int hertzInterval = 1000;
var freqScale = new FrequencyScale(nyquist, frameSize, hertzInterval);
var fst = freqScale.ScaleType;
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
sonogram.Configuration.WindowSize = freqScale.WindowSize;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst, freqScale.GridLineLocations);
image.Save(outputImagePath);
var expected = new[, ]
{
{ 46, 1000 },
{ 92, 2000 },
{ 139, 3000 },
{ 185, 4000 },
{ 232, 5000 },
{ 278, 6000 },
{ 325, 7000 },
{ 371, 8000 },
{ 417, 9000 },
{ 464, 10000 },
{ 510, 11000 },
};
Assert.That.MatricesAreEqual(expected, freqScale.GridLineLocations);
// Check that image dimensions are correct
Assert.AreEqual(566, image.Height);
Assert.AreEqual(1621, image.Width);
}
public void TestAnnotatedSonogramWithPlots()
{
// Make a decibel spectrogram
var actualDecibelSpectrogram = new SpectrogramStandard(this.sonoConfig, this.recording.WavReader);
// prepare normalisation bounds for three plots
double minDecibels = -100.0;
double maxDecibels = -50;
//double decibelThreshold = 12.5 dB above -100 dB;
var normThreshold = 0.25;
//plot 1
int minHz = 2000;
int maxHz = 3000;
var decibelArray = SNR.CalculateFreqBandAvIntensity(actualDecibelSpectrogram.Data, minHz, maxHz, actualDecibelSpectrogram.NyquistFrequency);
var normalisedIntensityArray = DataTools.NormaliseInZeroOne(decibelArray, minDecibels, maxDecibels);
var plot1 = new Plot("Intensity 2-3 kHz", normalisedIntensityArray, normThreshold);
//plot 2
minHz = 3000;
maxHz = 4000;
decibelArray = SNR.CalculateFreqBandAvIntensity(actualDecibelSpectrogram.Data, minHz, maxHz, actualDecibelSpectrogram.NyquistFrequency);
normalisedIntensityArray = DataTools.NormaliseInZeroOne(decibelArray, minDecibels, maxDecibels);
var plot2 = new Plot("Intensity 3-4 kHz", normalisedIntensityArray, normThreshold);
//plot 3
minHz = 4000;
maxHz = 5000;
decibelArray = SNR.CalculateFreqBandAvIntensity(actualDecibelSpectrogram.Data, minHz, maxHz, actualDecibelSpectrogram.NyquistFrequency);
normalisedIntensityArray = DataTools.NormaliseInZeroOne(decibelArray, minDecibels, maxDecibels);
var plot3 = new Plot("Intensity 4-5 kHz", normalisedIntensityArray, normThreshold);
// combine the plots
var plots = new List <Plot> {
plot1, plot2, plot3
};
// create three events
var startOffset = TimeSpan.Zero;
var events = new List <AcousticEvent>
{
new AcousticEvent(startOffset, 10.0, 10.0, 2000, 3000),
new AcousticEvent(startOffset, 25.0, 10.0, 3000, 4000),
new AcousticEvent(startOffset, 40.0, 10.0, 4000, 5000),
};
var image = SpectrogramTools.GetSonogramPlusCharts(actualDecibelSpectrogram, events, plots, null);
// create the image for visual confirmation
image.Save(Path.Combine(this.outputDirectory.FullName, this.recording.BaseName + ".png"));
Assert.AreEqual(1621, image.Width);
Assert.AreEqual(647, image.Height);
}
public void LinearFrequencyScaleDefault()
{
var recordingPath = PathHelper.ResolveAsset("Recordings", "BAC2_20071008-085040.wav");
var outputImagePath = this.outputDirectory.CombineFile("DefaultLinearScaleSonogram.png");
var recording = new AudioRecording(recordingPath);
// default linear scale
var fst = FreqScaleType.Linear;
var freqScale = new FrequencyScale(fst);
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
sonogram.Configuration.WindowSize = freqScale.WindowSize;
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst, freqScale.GridLineLocations);
image.Save(outputImagePath);
// Check that freqScale.GridLineLocations are correct
var expected = new[, ]
{
{ 23, 1000 },
{ 46, 2000 },
{ 69, 3000 },
{ 92, 4000 },
{ 116, 5000 },
{ 139, 6000 },
{ 162, 7000 },
{ 185, 8000 },
{ 208, 9000 },
{ 232, 10000 },
{ 255, 11000 },
};
Assert.That.MatricesAreEqual(expected, freqScale.GridLineLocations);
// Check that image dimensions are correct
Assert.AreEqual(310, image.Height);
Assert.AreEqual(3247, image.Width);
}
} //Analysis()
public static Tuple <List <Dictionary <string, double> >, double[]> DetectGratingEvents(double[,] matrix, int colStep, double intensityThreshold)
{
bool doNoiseremoval = true;
int minPeriod = 2; //both period values must be even numbers
int maxPeriod = 20; //Note: 17.2 frames per second i.e. period=20 is just over 1s.
int numberOfCycles = 4;
int step = 1;
int rowCount = matrix.GetLength(0);
int colCount = matrix.GetLength(1);
int numberOfColSteps = colCount / colStep;
var events2return = new List <Dictionary <string, double> >();
double[] array2return = null;
for (int b = 0; b < numberOfColSteps; b++)
{
int minCol = (b * colStep);
int maxCol = minCol + colStep - 1;
double[,] subMatrix = MatrixTools.Submatrix(matrix, 0, minCol, (rowCount - 1), maxCol);
double[] amplitudeArray = MatrixTools.GetRowAverages(subMatrix);
if (doNoiseremoval)
{
double StandardDeviationCount = 0.1; // number of noise SDs to calculate noise threshold - determines severity of noise reduction
SNR.BackgroundNoise bgn = SNR.SubtractBackgroundNoiseFromSignal(amplitudeArray, StandardDeviationCount);
amplitudeArray = bgn.NoiseReducedSignal;
}
//var events = CrossCorrelation.DetectBarsEventsBySegmentationAndXcorrelation(amplitudeArray, intensityThreshold);
var scores = Gratings.ScanArrayForGratingPattern(amplitudeArray, minPeriod, maxPeriod, numberOfCycles, step);
var mergedOutput = Gratings.MergePeriodicScoreArrays(scores, minPeriod, maxPeriod);
double[] intensity = mergedOutput.Item1;
double[] periodicity = mergedOutput.Item2;
var events = Gratings.ExtractPeriodicEvents(intensity, periodicity, intensityThreshold);
foreach (Dictionary <string, double> item in events)
{
item[key_MIN_FREQBIN] = minCol;
item[key_MAX_FREQBIN] = maxCol;
events2return.Add(item);
}
if (b == 3)
{
array2return = amplitudeArray; //returned for debugging purposes only
}
} //for loop over bands of columns
return(Tuple.Create(events2return, array2return));
}//end DetectGratingEvents()
private double[,] SobelEdgegram(double[,] matrix)
{
double[,] m = MFCCStuff.DecibelSpectra(matrix, this.Configuration.WindowPower, this.SampleRate, this.Configuration.epsilon); //from spectrogram
//double[,] m = Speech.DecibelSpectra(matrix);
//NOISE REDUCTION
var output = SNR.NoiseReduce(m, this.Configuration.NoiseReductionType, this.Configuration.NoiseReductionParameter);
this.SnrData.ModalNoiseProfile = output.Item2;
return(ImageTools.SobelEdgeDetection(output.Item1));
}
public static AudioToSonogramResult AnalyseOneRecording(
FileInfo sourceRecording,
Dictionary <string, string> configDict,
TimeSpan localEventStart,
TimeSpan localEventEnd,
int minHz,
int maxHz,
DirectoryInfo outDirectory)
{
// set a threshold for determining energy distribution in call
// NOTE: value of this threshold depends on whether working with decibel, energy or amplitude values
const double threshold = 9.0;
int resampleRate = AppConfigHelper.DefaultTargetSampleRate;
if (configDict.ContainsKey(AnalysisKeys.ResampleRate))
{
resampleRate = int.Parse(configDict[AnalysisKeys.ResampleRate]);
}
configDict[ConfigKeys.Recording.Key_RecordingCallName] = sourceRecording.FullName;
configDict[ConfigKeys.Recording.Key_RecordingFileName] = sourceRecording.Name;
// 1: GET RECORDING and make temporary copy
// put temp audio FileSegment in same directory as the required output image.
var tempAudioSegment = TempFileHelper.NewTempFile(outDirectory, "wav");
// delete the temp audio file if it already exists.
if (File.Exists(tempAudioSegment.FullName))
{
File.Delete(tempAudioSegment.FullName);
}
// This line creates a temporary version of the source file downsampled as per entry in the config file
MasterAudioUtility.SegmentToWav(sourceRecording, tempAudioSegment, new AudioUtilityRequest()
{
TargetSampleRate = resampleRate
});
// 2: Generate sonogram image files
AudioToSonogramResult result = GenerateSpectrogramImages(tempAudioSegment, configDict, outDirectory);
// 3: GET the SNR statistics
TimeSpan eventDuration = localEventEnd - localEventStart;
result.SnrStatistics = SNR.Calculate_SNR_ShortRecording(tempAudioSegment, configDict, localEventStart, eventDuration, minHz, maxHz, threshold);
// 4: Delete the temp file
File.Delete(tempAudioSegment.FullName);
return(result);
}
public static Tuple <BaseSonogram, AcousticEvent, double[, ], double[], double[, ]> Execute_Extraction(
AudioRecording recording,
double eventStart,
double eventEnd,
int minHz,
int maxHz,
double frameOverlap,
double backgroundThreshold,
TimeSpan segmentStartOffset)
{
//ii: MAKE SONOGRAM
SonogramConfig sonoConfig = new SonogramConfig(); //default values config
sonoConfig.SourceFName = recording.BaseName;
//sonoConfig.WindowSize = windowSize;
sonoConfig.WindowOverlap = frameOverlap;
BaseSonogram sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
Log.WriteLine("Frames: Size={0}, Count={1}, Duration={2:f1}ms, Overlap={5:f2}%, Offset={3:f1}ms, Frames/s={4:f1}",
sonogram.Configuration.WindowSize, sonogram.FrameCount, (sonogram.FrameDuration * 1000),
(sonogram.FrameStep * 1000), sonogram.FramesPerSecond, frameOverlap);
int binCount = (int)(maxHz / sonogram.FBinWidth) - (int)(minHz / sonogram.FBinWidth) + 1;
Log.WriteIfVerbose("Freq band: {0} Hz - {1} Hz. (Freq bin count = {2})", minHz, maxHz, binCount);
//calculate the modal noise profile
double SD_COUNT = 0.0; // number of noise standard deviations used to calculate noise threshold
NoiseProfile profile = NoiseProfile.CalculateModalNoiseProfile(sonogram.Data, SD_COUNT); //calculate modal noise profile
double[] modalNoise = DataTools.filterMovingAverage(profile.NoiseMode, 7); //smooth the noise profile
//extract modal noise values of the required event
double[] noiseSubband = SpectrogramTools.ExtractModalNoiseSubband(modalNoise, minHz, maxHz, false, sonogram.NyquistFrequency, sonogram.FBinWidth);
//extract data values of the required event
double[,] target = SpectrogramTools.ExtractEvent(sonogram.Data, eventStart, eventEnd, sonogram.FrameStep,
minHz, maxHz, false, sonogram.NyquistFrequency, sonogram.FBinWidth);
// create acoustic event with defined boundaries
AcousticEvent ae = new AcousticEvent(segmentStartOffset, eventStart, eventEnd - eventStart, minHz, maxHz);
ae.SetTimeAndFreqScales(sonogram.FramesPerSecond, sonogram.FBinWidth);
//truncate noise
sonogram.Data = SNR.TruncateBgNoiseFromSpectrogram(sonogram.Data, modalNoise);
sonogram.Data = SNR.RemoveNeighbourhoodBackgroundNoise(sonogram.Data, backgroundThreshold);
double[,] targetMinusNoise = SpectrogramTools.ExtractEvent(sonogram.Data, eventStart, eventEnd, sonogram.FrameStep,
minHz, maxHz, false, sonogram.NyquistFrequency, sonogram.FBinWidth);
return(Tuple.Create(sonogram, ae, target, noiseSubband, targetMinusNoise));
}
/// <summary>
/// METHOD TO CHECK IF SPECIFIED linear FREQ SCALE IS WORKING
/// Check it on standard one minute recording.
/// </summary>
public static void TESTMETHOD_LinearFrequencyScale()
{
var recordingPath = @"C:\SensorNetworks\SoftwareTests\TestRecordings\BAC2_20071008-085040.wav";
var outputDir = @"C:\SensorNetworks\SoftwareTests\TestFrequencyScale".ToDirectoryInfo();
var expectedResultsDir = Path.Combine(outputDir.FullName, TestTools.ExpectedResultsDir).ToDirectoryInfo();
var outputImagePath = Path.Combine(outputDir.FullName, "linearScaleSonogram.png");
var opFileStem = "BAC2_20071008";
var recording = new AudioRecording(recordingPath);
// specfied linear scale
int nyquist = 11025;
int frameSize = 1024;
int hertzInterval = 1000;
var freqScale = new FrequencyScale(nyquist, frameSize, hertzInterval);
var fst = freqScale.ScaleType;
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
//NoiseReductionType = NoiseReductionType.Standard,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
sonogram.Configuration.WindowSize = freqScale.WindowSize;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
image.Save(outputImagePath);
// DO FILE EQUALITY TEST
string testName = "testName";
var expectedTestFile = new FileInfo(Path.Combine(expectedResultsDir.FullName, "FrequencyLinearScaleTest.EXPECTED.json"));
var resultFile = new FileInfo(Path.Combine(outputDir.FullName, opFileStem + "FrequencyLinearScaleTestResults.json"));
Acoustics.Shared.Csv.Csv.WriteMatrixToCsv(resultFile, freqScale.GridLineLocations);
TestTools.FileEqualityTest(testName, resultFile, expectedTestFile);
LoggedConsole.WriteLine("Completed Linear Frequency Scale test");
Console.WriteLine("\n\n");
}
/// <summary>
/// 10-percentile Noise Reduction
/// </summary>
public static double[,] NoiseReduction(double[,] matrix)
{
double[,] nrm = matrix;
// calculate 10-percentile noise profile
NoiseProfile profile = NoiseProfile.CalculatePercentileNoiseProfile(matrix, 10);
// smooth the noise profile
double[] smoothedProfile = DataTools.filterMovingAverage(profile.NoiseThresholds, width: 7);
nrm = SNR.TruncateBgNoiseFromSpectrogram(nrm, smoothedProfile);
return(nrm);
}
public static double[,] GetDecibelSpectrogramNoiseReduced(AudioRecording recording, int frameSize)
{
int frameStep = frameSize;
// get decibel spectrogram
var results = DSP_Frames.ExtractEnvelopeAndAmplSpectrogram(recording.WavReader.Samples, recording.SampleRate, recording.Epsilon, frameSize, frameStep);
var spectrogram = MFCCStuff.DecibelSpectra(results.AmplitudeSpectrogram, results.WindowPower, recording.SampleRate, recording.Epsilon);
// remove background noise from spectrogram
double[] spectralDecibelBgn = NoiseProfile.CalculateBackgroundNoise(spectrogram);
spectrogram = SNR.TruncateBgNoiseFromSpectrogram(spectrogram, spectralDecibelBgn);
spectrogram = SNR.RemoveNeighbourhoodBackgroundNoise(spectrogram, nhThreshold: 3.0);
return(spectrogram);
}
/// <summary>
/// A FALSE-COLOUR VERSION OF DECIBEL SPECTROGRAM
/// Taken and adapted from Spectrogram Image 5 in the method of CLASS Audio2InputForConvCNN.cs:.
/// </summary>
/// <param name="dbSpectrogramData">the sonogram data (NOT noise reduced). </param>
public static Image <Rgb24> DrawStandardSpectrogramInFalseColour(double[,] dbSpectrogramData)
{
// Do NOISE REDUCTION
double noiseReductionParameter = 2.0;
var tuple = SNR.NoiseReduce(dbSpectrogramData, NoiseReductionType.Standard, noiseReductionParameter);
double[,] nrSpectrogramData = tuple.Item1; // store data matrix
double ridgeThreshold = 2.5;
double[,] matrix = dbSpectrogramData;
byte[,] hits = RidgeDetection.Sobel5X5RidgeDetectionExperiment(matrix, ridgeThreshold);
// ################### RESEARCH QUESTION:
// I tried different EXPERIMENTS IN NORMALISATION
//double min; double max;
//DataTools.MinMax(spectralSelection, out min, out max);
//double range = max - min;
// readjust min and max to create the effect of contrast stretching. It enhances the spectrogram a bit
//double fractionalStretching = 0.2;
//min = min + (range * fractionalStretching);
//max = max - (range * fractionalStretching);
//range = max - min;
// ULTIMATELY THE BEST APPROACH APPEARED TO BE FIXED NORMALISATION BOUNDS
double truncateMin = -95.0;
double truncateMax = -30.0;
double filterCoefficient = 0.75;
double[,] dbSpectrogramNorm = SpectrogramTools.NormaliseSpectrogramMatrix(dbSpectrogramData, truncateMin, truncateMax, filterCoefficient);
truncateMin = 0;
truncateMax = 50;
// nr = noise reduced
double[,] nrSpectrogramNorm = SpectrogramTools.NormaliseSpectrogramMatrix(nrSpectrogramData, truncateMin, truncateMax, filterCoefficient);
nrSpectrogramNorm = MatrixTools.BoundMatrix(nrSpectrogramNorm, 0.0, 0.9);
nrSpectrogramNorm = MatrixTools.SquareRootOfValues(nrSpectrogramNorm);
nrSpectrogramNorm = DataTools.normalise(nrSpectrogramNorm);
// create image from normalised data
var image = SpectrogramTools.CreateFalseColourDecibelSpectrogramForZooming(dbSpectrogramNorm, nrSpectrogramNorm, hits);
return(image);
}
/// <summary>
/// METHOD TO CHECK IF Octave FREQ SCALE IS WORKING
/// Check it on MARINE RECORDING from JASCO, SR=64000.
/// 24 BIT JASCO RECORDINGS from GBR must be converted to 16 bit.
/// ffmpeg -i source_file.wav -sample_fmt s16 out_file.wav
/// e.g. ". C:\Work\Github\audio-analysis\Extra Assemblies\ffmpeg\ffmpeg.exe" -i "C:\SensorNetworks\WavFiles\MarineRecordings\JascoGBR\AMAR119-00000139.00000139.Chan_1-24bps.1375012796.2013-07-28-11-59-56.wav" -sample_fmt s16 "C:\SensorNetworks\Output\OctaveFreqScale\JascoeMarineGBR116bit.wav"
/// ffmpeg binaries are in C:\Work\Github\audio-analysis\Extra Assemblies\ffmpeg
/// </summary>
public static void TESTMETHOD_OctaveFrequencyScale2()
{
var recordingPath = @"C:\SensorNetworks\SoftwareTests\TestRecordings\MarineJasco_AMAR119-00000139.00000139.Chan_1-24bps.1375012796.2013-07-28-11-59-56-16bit.wav";
var outputDir = @"C:\SensorNetworks\SoftwareTests\TestFrequencyScale".ToDirectoryInfo();
var expectedResultsDir = Path.Combine(outputDir.FullName, TestTools.ExpectedResultsDir).ToDirectoryInfo();
var outputImagePath = Path.Combine(outputDir.FullName, "JascoMarineGBR1.png");
var opFileStem = "JascoMarineGBR1";
var recording = new AudioRecording(recordingPath);
var fst = FreqScaleType.Linear125Octaves7Tones28Nyquist32000;
var freqScale = new FrequencyScale(fst);
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.WindowSize,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
var sonogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
sonogram.Data = OctaveFreqScale.ConvertAmplitudeSpectrogramToDecibelOctaveScale(sonogram.Data, freqScale);
// DO NOISE REDUCTION
var dataMatrix = SNR.NoiseReduce_Standard(sonogram.Data);
sonogram.Data = dataMatrix;
sonogram.Configuration.WindowSize = freqScale.WindowSize;
var image = sonogram.GetImageFullyAnnotated(sonogram.GetImage(), "SPECTROGRAM: " + fst.ToString(), freqScale.GridLineLocations);
image.Save(outputImagePath);
// DO FILE EQUALITY TEST
string testName = "test2";
var expectedTestFile = new FileInfo(Path.Combine(expectedResultsDir.FullName, "FrequencyOctaveScaleTest2.EXPECTED.json"));
var resultFile = new FileInfo(Path.Combine(outputDir.FullName, opFileStem + "FrequencyOctaveScaleTest2Results.json"));
Acoustics.Shared.Csv.Csv.WriteMatrixToCsv(resultFile, freqScale.GridLineLocations);
TestTools.FileEqualityTest(testName, resultFile, expectedTestFile);
LoggedConsole.WriteLine("Completed Octave Frequency Scale " + testName);
Console.WriteLine("\n\n");
}
/// <summary>
/// This method produces four spectrograms using four different values of neighbour hood decibel threshold.
/// It can be used for test purposes.
/// </summary>
/// <param name="deciBelSpectrogram">the noisy decibel spectrogram</param>
/// <param name="xAxisInterval">x-axis tic interval</param>
/// <param name="stepDuration">the x-axis times scale</param>
/// <param name="nyquist">max freq value</param>
/// <param name="hzInterval">y-axis frequency scale</param>
/// <returns>Image containing four sepctrograms</returns>
public static Image ModalNoiseRemovalAndGetSonograms(
double[,] deciBelSpectrogram,
TimeSpan xAxisInterval,
TimeSpan stepDuration,
int nyquist,
int hzInterval)
{
// The number of SDs above the mean for noise removal.
// Set sdCount = -0.5 becuase when sdCount >= zero, noies removal is a bit severe for environmental recordings.
var sdCount = -0.5;
var nrt = NoiseReductionType.Modal;
var tuple = SNR.NoiseReduce(deciBelSpectrogram, nrt, sdCount);
var noiseReducedSpectrogram1 = tuple.Item1;
var title = "title1";
var image1 = DrawSonogram(noiseReducedSpectrogram1, xAxisInterval, stepDuration, nyquist, hzInterval, title);
double dBThreshold = 0.0; // SPECTRAL dB THRESHOLD for smoothing background
double[,] noiseReducedSpectrogram2 = SNR.RemoveNeighbourhoodBackgroundNoise(noiseReducedSpectrogram1, dBThreshold);
title = "title2";
var image2 = DrawSonogram(noiseReducedSpectrogram2, xAxisInterval, stepDuration, nyquist, hzInterval, title);
// SPECTRAL dB THRESHOLD for smoothing background
dBThreshold = 3.0;
noiseReducedSpectrogram2 = SNR.RemoveNeighbourhoodBackgroundNoise(noiseReducedSpectrogram1, dBThreshold);
title = "title3";
var image3 = DrawSonogram(noiseReducedSpectrogram2, xAxisInterval, stepDuration, nyquist, hzInterval, title);
// SPECTRAL dB THRESHOLD for smoothing background
dBThreshold = 10.0;
noiseReducedSpectrogram2 = SNR.RemoveNeighbourhoodBackgroundNoise(noiseReducedSpectrogram1, dBThreshold);
title = "title4";
var image4 = DrawSonogram(noiseReducedSpectrogram2, xAxisInterval, stepDuration, nyquist, hzInterval, title);
var array = new Image[4];
array[0] = image1;
array[1] = image2;
array[2] = image3;
array[3] = image4;
var combinedImage = ImageTools.CombineImagesVertically(array);
return(combinedImage);
}
/// <summary>
/// Median Noise Reduction
/// </summary>
public static double[,] NoiseReduction(double[,] matrix)
{
double[,] nrm = matrix;
// calculate modal noise profile
// NoiseProfile profile = NoiseProfile.CalculateModalNoiseProfile(matrix, sdCount: 0.0);
NoiseProfile profile = NoiseProfile.CalculateMedianNoiseProfile(matrix);
// smooth the noise profile
double[] smoothedProfile = DataTools.filterMovingAverage(profile.NoiseThresholds, width: 7);
nrm = SNR.TruncateBgNoiseFromSpectrogram(nrm, smoothedProfile);
// nrm = SNR.NoiseReduce_Standard(nrm, smoothedProfile, nhBackgroundThreshold: 2.0);
return(nrm);
}
public static double[,] GetAmplitudeSpectrogramNoiseReduced(AudioRecording recording, int frameSize)
{
int frameStep = frameSize;
// get amplitude spectrogram and remove the DC column ie column zero.
var results = DSP_Frames.ExtractEnvelopeAndAmplSpectrogram(recording.WavReader.Samples, recording.SampleRate, recording.Epsilon, frameSize, frameStep);
// remove background noise from the full amplitude spectrogram
const double sdCount = 0.1;
const double spectralBgThreshold = 0.003; // SPECTRAL AMPLITUDE THRESHOLD for smoothing background
var profile = NoiseProfile.CalculateModalNoiseProfile(results.AmplitudeSpectrogram, sdCount); //calculate noise profile - assumes a dB spectrogram.
double[] noiseValues = DataTools.filterMovingAverage(profile.NoiseThresholds, 7); // smooth the noise profile
var amplitudeSpectrogram = SNR.NoiseReduce_Standard(results.AmplitudeSpectrogram, noiseValues, spectralBgThreshold);
return(amplitudeSpectrogram);
}
/// <summary>
/// Initializes a new instance of the <see cref="DecibelSpectrogram"/> class.
/// </summary>
public DecibelSpectrogram(AmplitudeSpectrogram amplitudeSpectrogram)
{
this.Configuration = amplitudeSpectrogram.Configuration;
this.Attributes = amplitudeSpectrogram.Attributes;
// (ii) CONVERT AMPLITUDES TO DECIBELS
this.Data = MFCCStuff.DecibelSpectra(amplitudeSpectrogram.Data, this.Attributes.WindowPower, this.Attributes.SampleRate, this.Attributes.Epsilon);
// (iii) NOISE REDUCTION
var tuple = SNR.NoiseReduce(this.Data, this.Configuration.NoiseReductionType, this.Configuration.NoiseReductionParameter);
this.Data = tuple.Item1; // store data matrix
if (this.SnrData != null)
{
this.SnrData.ModalNoiseProfile = tuple.Item2; // store the full bandwidth modal noise profile
}
}
public void TestGetEventsAroundMaxima()
{
//string abbreviatedSpeciesName = "Pteropus";
string speciesName = "Pteropus species";
int minHz = 800;
int maxHz = 8000;
var minTimeSpan = TimeSpan.FromSeconds(0.15);
var maxTimeSpan = TimeSpan.FromSeconds(0.8);
double decibelThreshold = 9.0;
TimeSpan segmentStartOffset = TimeSpan.Zero;
var decibelArray = SNR.CalculateFreqBandAvIntensity(this.sonogram.Data, minHz, maxHz, this.sonogram.NyquistFrequency);
// prepare plots
double intensityNormalisationMax = 3 * decibelThreshold;
var eventThreshold = decibelThreshold / intensityNormalisationMax;
var normalisedIntensityArray = DataTools.NormaliseInZeroOne(decibelArray, 0, intensityNormalisationMax);
var plot = new Plot(speciesName + " Territory", normalisedIntensityArray, eventThreshold);
var plots = new List <Plot> {
plot
};
//iii: CONVERT decibel SCORES TO ACOUSTIC EVENTS
var acousticEvents = AcousticEvent.GetEventsAroundMaxima(
decibelArray,
segmentStartOffset,
minHz,
maxHz,
decibelThreshold,
minTimeSpan,
maxTimeSpan,
this.sonogram.FramesPerSecond,
this.sonogram.FBinWidth);
Assert.AreEqual(10, acousticEvents.Count);
Assert.AreEqual(new Rectangle(19, 1751, 168, 27), acousticEvents[0].GetEventAsRectangle());
Assert.AreEqual(new Rectangle(19, 1840, 168, 10), acousticEvents[2].GetEventAsRectangle());
Assert.AreEqual(new Rectangle(19, 1961, 168, 31), acousticEvents[5].GetEventAsRectangle());
Assert.AreEqual(new Rectangle(19, 2294, 168, 17), acousticEvents[7].GetEventAsRectangle());
Assert.AreEqual(new Rectangle(19, 2504, 168, 7), acousticEvents[9].GetEventAsRectangle());
//Assert.AreEqual(28.Seconds() + segmentOffset, stats.ResultStartSeconds.Seconds());
}
public void PcaWhiteningDefault()
{
var recordingPath = PathHelper.ResolveAsset("Recordings", "BAC2_20071008-085040.wav");
var fst = FreqScaleType.Linear;
var freqScale = new FrequencyScale(fst);
var recording = new AudioRecording(recordingPath);
var sonoConfig = new SonogramConfig
{
WindowSize = freqScale.FinalBinCount * 2,
WindowOverlap = 0.2,
SourceFName = recording.BaseName,
NoiseReductionType = NoiseReductionType.None,
NoiseReductionParameter = 0.0,
};
// GENERATE AMPLITUDE SPECTROGRAM
var spectrogram = new AmplitudeSonogram(sonoConfig, recording.WavReader);
spectrogram.Configuration.WindowSize = freqScale.WindowSize;
// DO RMS NORMALIZATION
spectrogram.Data = SNR.RmsNormalization(spectrogram.Data);
// CONVERT NORMALIZED AMPLITUDE SPECTROGRAM TO dB SPECTROGRAM
var sonogram = new SpectrogramStandard(spectrogram);
// DO NOISE REDUCTION
var dataMatrix = PcaWhitening.NoiseReduction(sonogram.Data);
sonogram.Data = dataMatrix;
// DO PCA WHITENING
var whitenedSpectrogram = PcaWhitening.Whitening(sonogram.Data);
// DO UNIT TESTING
// check if the dimensions of the reverted spectrogram (second output of the pca whitening) is equal to the input matrix
Assert.AreEqual(whitenedSpectrogram.Reversion.GetLength(0), sonogram.Data.GetLength(0));
Assert.AreEqual(whitenedSpectrogram.Reversion.GetLength(1), sonogram.Data.GetLength(1));
}
} // LocalPeaks()
/// <summary>
/// CALCULATEs SPECTRAL PEAK TRACKS: spectralIndices.SPT, RHZ, RVT, RPS, RNG
/// This method is only called from IndexCalulate.analysis() when the IndexCalculation Duration is less than 10 seconds,
/// because need to recalculate background noise etc.
/// Otherwise the constructor of this class is called: sptInfo = new SpectralPeakTracks(decibelSpectrogram, peakThreshold);
/// NOTE: We require a noise reduced decibel spectrogram
/// FreqBinWidth can be accessed, if required, through dspOutput1.FreqBinWidth.
/// </summary>
public static SpectralPeakTracks CalculateSpectralPeakTracks(AudioRecording recording, int sampleStart, int sampleEnd, int frameSize, bool octaveScale, double peakThreshold)
{
double epsilon = recording.Epsilon;
int sampleRate = recording.WavReader.SampleRate;
int bufferFrameCount = 2; // 2 because must allow for edge effects when using 5x5 grid to find ridges.
int ridgeBuffer = frameSize * bufferFrameCount;
var ridgeRecording = AudioRecording.GetRecordingSubsegment(recording, sampleStart, sampleEnd, ridgeBuffer);
int frameStep = frameSize;
var dspOutput = DSP_Frames.ExtractEnvelopeAndFfts(ridgeRecording, frameSize, frameStep);
// Generate the ridge SUBSEGMENT deciBel spectrogram from the SUBSEGMENT amplitude spectrogram
// i: generate the SUBSEGMENT deciBel spectrogram from the SUBSEGMENT amplitude spectrogram
double[,] decibelSpectrogram;
if (octaveScale)
{
var freqScale = new FrequencyScale(FreqScaleType.Linear125Octaves7Tones28Nyquist32000);
decibelSpectrogram = OctaveFreqScale.DecibelSpectra(dspOutput.AmplitudeSpectrogram, dspOutput.WindowPower, sampleRate, epsilon, freqScale);
}
else
{
decibelSpectrogram = MFCCStuff.DecibelSpectra(dspOutput.AmplitudeSpectrogram, dspOutput.WindowPower, sampleRate, epsilon);
}
// calculate the noise profile
var spectralDecibelBgn = NoiseProfile.CalculateBackgroundNoise(decibelSpectrogram);
decibelSpectrogram = SNR.TruncateBgNoiseFromSpectrogram(decibelSpectrogram, spectralDecibelBgn);
double nhDecibelThreshold = 2.0; // SPECTRAL dB THRESHOLD for smoothing background
decibelSpectrogram = SNR.RemoveNeighbourhoodBackgroundNoise(decibelSpectrogram, nhDecibelThreshold);
// thresholds in decibels
// double frameStepDuration = frameStep / (double)sampleRate; // fraction of a second
// TimeSpan frameStepTimeSpan = TimeSpan.FromTicks((long)(frameStepDuration * TimeSpan.TicksPerSecond));
var sptInfo = new SpectralPeakTracks(decibelSpectrogram, peakThreshold);
return(sptInfo);
}
/// <summary>
/// This method normalizes a score array by subtracting the mode rather than the average of the array.
/// This is because the noise is often not normally distributed but rather skewed.
/// However, did not work well.
/// </summary>
public static List <Plot> SubtractModeAndSd(List <Plot> plots)
{
var opPlots = new List <Plot>();
// subtract average from each plot array
foreach (var plot in plots)
{
var scores = plot.data;
var bgn = SNR.CalculateModalBackgroundNoiseInSignal(scores, 1.0);
var mode = bgn.NoiseMode;
var sd = bgn.NoiseSd;
// normalize the scores to z-scores
for (int i = 0; i < scores.Length; i++)
{
// Convert scores to z-scores
scores[i] = (scores[i] - mode) / sd;
if (scores[i] < 0.0)
{
scores[i] = 0.0;
}
if (scores[i] > 4.0)
{
scores[i] = 4.0;
}
// normalize full scale to 4 SDs.
scores[i] /= 4.0;
}
opPlots.Add(plot);
}
return(opPlots);
}
}//end CONSTRUCTOR
public override void Make(double[,] amplitudeM)
{
double[,] m = amplitudeM;
// (i) IF REQUIRED CONVERT TO FULL BAND WIDTH MEL SCALE
// Make sure you have Configuration.MelBinCount somewhere
if (this.Configuration.DoMelScale)
{
m = MFCCStuff.MelFilterBank(m, this.Configuration.MelBinCount, this.NyquistFrequency, 0, this.NyquistFrequency); // using the Greg integral
}
// (ii) CONVERT AMPLITUDES TO DECIBELS
m = MFCCStuff.DecibelSpectra(m, this.Configuration.WindowPower, this.SampleRate, this.Configuration.epsilon);
// (iii) NOISE REDUCTION
var tuple = SNR.NoiseReduce(m, this.Configuration.NoiseReductionType, this.Configuration.NoiseReductionParameter);
this.Data = tuple.Item1; // store data matrix
if (this.SnrData != null)
{
this.SnrData.ModalNoiseProfile = tuple.Item2; // store the full bandwidth modal noise profile
}
}
/// <summary>
/// The CORE ANALYSIS METHOD.
/// </summary>
public static Tuple <BaseSonogram, double[, ], Plot, List <AcousticEvent>, TimeSpan> Analysis(FileInfo fiSegmentOfSourceFile, Dictionary <string, string> configDict, TimeSpan segmentStartOffset)
{
//set default values -
int frameLength = 1024;
if (configDict.ContainsKey(AnalysisKeys.FrameLength))
{
frameLength = int.Parse(configDict[AnalysisKeys.FrameLength]);
}
double windowOverlap = 0.0;
int minHz = int.Parse(configDict["MIN_HZ"]);
int minFormantgap = int.Parse(configDict["MIN_FORMANT_GAP"]);
int maxFormantgap = int.Parse(configDict["MAX_FORMANT_GAP"]);
double decibelThreshold = double.Parse(configDict["DECIBEL_THRESHOLD"]); //dB
double harmonicIntensityThreshold = double.Parse(configDict["INTENSITY_THRESHOLD"]); //in 0-1
double callDuration = double.Parse(configDict["CALL_DURATION"]); // seconds
AudioRecording recording = new AudioRecording(fiSegmentOfSourceFile.FullName);
//i: MAKE SONOGRAM
var sonoConfig = new SonogramConfig
{
SourceFName = recording.BaseName,
WindowSize = frameLength,
WindowOverlap = windowOverlap,
NoiseReductionType = SNR.KeyToNoiseReductionType("STANDARD"),
}; //default values config
TimeSpan tsRecordingtDuration = recording.Duration;
int sr = recording.SampleRate;
double freqBinWidth = sr / (double)sonoConfig.WindowSize;
double framesPerSecond = freqBinWidth;
//the Xcorrelation-FFT technique requires number of bins to scan to be power of 2.
//assuming sr=17640 and window=1024, then 64 bins span 1100 Hz above the min Hz level. i.e. 500 to 1600
//assuming sr=17640 and window=1024, then 128 bins span 2200 Hz above the min Hz level. i.e. 500 to 2700
int numberOfBins = 64;
int minBin = (int)Math.Round(minHz / freqBinWidth) + 1;
int maxbin = minBin + numberOfBins - 1;
int maxHz = (int)Math.Round(minHz + (numberOfBins * freqBinWidth));
BaseSonogram sonogram = new SpectrogramStandard(sonoConfig, recording.WavReader);
int rowCount = sonogram.Data.GetLength(0);
int colCount = sonogram.Data.GetLength(1);
double[,] subMatrix = MatrixTools.Submatrix(sonogram.Data, 0, minBin, rowCount - 1, maxbin);
int callSpan = (int)Math.Round(callDuration * framesPerSecond);
//#############################################################################################################################################
//ii: DETECT HARMONICS
var results = CrossCorrelation.DetectHarmonicsInSonogramMatrix(subMatrix, decibelThreshold, callSpan);
double[] dBArray = results.Item1;
double[] intensity = results.Item2; //an array of periodicity scores
double[] periodicity = results.Item3;
//intensity = DataTools.filterMovingAverage(intensity, 3);
int noiseBound = (int)(100 / freqBinWidth); //ignore 0-100 hz - too much noise
double[] scoreArray = new double[intensity.Length];
for (int r = 0; r < rowCount; r++)
{
if (intensity[r] < harmonicIntensityThreshold)
{
continue;
}
//ignore locations with incorrect formant gap
double herzPeriod = periodicity[r] * freqBinWidth;
if (herzPeriod < minFormantgap || herzPeriod > maxFormantgap)
{
continue;
}
//find freq having max power and use info to adjust score.
//expect humans to have max < 1000 Hz
double[] spectrum = MatrixTools.GetRow(sonogram.Data, r);
for (int j = 0; j < noiseBound; j++)
{
spectrum[j] = 0.0;
}
int maxIndex = DataTools.GetMaxIndex(spectrum);
int freqWithMaxPower = (int)Math.Round(maxIndex * freqBinWidth);
double discount = 1.0;
if (freqWithMaxPower < 1200)
{
discount = 0.0;
}
if (intensity[r] > harmonicIntensityThreshold)
{
scoreArray[r] = intensity[r] * discount;
}
}
//transfer info to a hits matrix.
var hits = new double[rowCount, colCount];
double threshold = harmonicIntensityThreshold * 0.75; //reduced threshold for display of hits
for (int r = 0; r < rowCount; r++)
{
if (scoreArray[r] < threshold)
{
continue;
}
double herzPeriod = periodicity[r] * freqBinWidth;
for (int c = minBin; c < maxbin; c++)
{
//hits[r, c] = herzPeriod / (double)380; //divide by 380 to get a relativePeriod;
hits[r, c] = (herzPeriod - minFormantgap) / maxFormantgap; //to get a relativePeriod;
}
}
//iii: CONVERT TO ACOUSTIC EVENTS
double maxPossibleScore = 0.5;
int halfCallSpan = callSpan / 2;
var predictedEvents = new List <AcousticEvent>();
for (int i = 0; i < rowCount; i++)
{
//assume one score position per crow call
if (scoreArray[i] < 0.001)
{
continue;
}
double startTime = (i - halfCallSpan) / framesPerSecond;
AcousticEvent ev = new AcousticEvent(segmentStartOffset, startTime, callDuration, minHz, maxHz);
ev.SetTimeAndFreqScales(framesPerSecond, freqBinWidth);
ev.Score = scoreArray[i];
ev.ScoreNormalised = ev.Score / maxPossibleScore; // normalised to the user supplied threshold
//ev.Score_MaxPossible = maxPossibleScore;
predictedEvents.Add(ev);
} //for loop
Plot plot = new Plot("CROW", intensity, harmonicIntensityThreshold);
return(Tuple.Create(sonogram, hits, plot, predictedEvents, tsRecordingtDuration));
} //Analysis()
//////public static IndexCalculateResult Analysis(
public static SpectralIndexValuesForContentDescription Analysis(
AudioRecording recording,
TimeSpan segmentOffsetTimeSpan,
int sampleRateOfOriginalAudioFile,
bool returnSonogramInfo = false)
{
// returnSonogramInfo = true; // if debugging
double epsilon = recording.Epsilon;
int sampleRate = recording.WavReader.SampleRate;
//var segmentDuration = TimeSpan.FromSeconds(recording.WavReader.Time.TotalSeconds);
var indexCalculationDuration = TimeSpan.FromSeconds(ContentSignatures.IndexCalculationDurationInSeconds);
// Get FRAME parameters for the calculation of Acoustic Indices
int frameSize = ContentSignatures.FrameSize;
int frameStep = frameSize; // that is, windowOverlap = zero
double frameStepDuration = frameStep / (double)sampleRate; // fraction of a second
var frameStepTimeSpan = TimeSpan.FromTicks((long)(frameStepDuration * TimeSpan.TicksPerSecond));
// INITIALISE a RESULTS STRUCTURE TO return
// initialize a result object in which to store SummaryIndexValues and SpectralIndexValues etc.
var config = new IndexCalculateConfig(); // sets some default values
int freqBinCount = frameSize / 2;
var indexProperties = GetIndexProperties();
////////var result = new IndexCalculateResult(freqBinCount, indexProperties, indexCalculationDuration, segmentOffsetTimeSpan, config);
var spectralIndices = new SpectralIndexValuesForContentDescription();
///////result.SummaryIndexValues = null;
///////SpectralIndexValues spectralIndices = result.SpectralIndexValues;
// set up default spectrogram to return
///////result.Sg = returnSonogramInfo ? GetSonogram(recording, windowSize: 1024) : null;
///////result.Hits = null;
///////result.TrackScores = new List<Plot>();
// ################################## FINISHED SET-UP
// ################################## NOW GET THE AMPLITUDE SPECTROGRAM
// EXTRACT ENVELOPE and SPECTROGRAM FROM RECORDING SEGMENT
// Note that the amplitude spectrogram has had the DC bin removed. i.e. has only 256 columns.
var dspOutput1 = DSP_Frames.ExtractEnvelopeAndFfts(recording, frameSize, frameStep);
var amplitudeSpectrogram = dspOutput1.AmplitudeSpectrogram;
// (B) ################################## EXTRACT OSC SPECTRAL INDEX DIRECTLY FROM THE RECORDING ##################################
// Get the oscillation spectral index OSC separately from signal because need a different frame size etc.
var sampleLength = Oscillations2014.DefaultSampleLength;
var frameLength = Oscillations2014.DefaultFrameLength;
var sensitivity = Oscillations2014.DefaultSensitivityThreshold;
var spectralIndexShort = Oscillations2014.GetSpectralIndex_Osc(recording, frameLength, sampleLength, sensitivity);
// double length of the vector because want to work with 256 element vector for spectrogram purposes
spectralIndices.OSC = DataTools.VectorDoubleLengthByAverageInterpolation(spectralIndexShort);
// (C) ################################## EXTRACT SPECTRAL INDICES FROM THE AMPLITUDE SPECTROGRAM ##################################
// IFF there has been UP-SAMPLING, calculate bin of the original audio nyquist. this will be less than SR/2.
// original sample rate can be anything 11.0-44.1 kHz.
int originalNyquist = sampleRateOfOriginalAudioFile / 2;
// if up-sampling has been done
if (dspOutput1.NyquistFreq > originalNyquist)
{
dspOutput1.NyquistFreq = originalNyquist;
dspOutput1.NyquistBin = (int)Math.Floor(originalNyquist / dspOutput1.FreqBinWidth); // note that bin width does not change
}
// ii: CALCULATE THE ACOUSTIC COMPLEXITY INDEX
spectralIndices.ACI = AcousticComplexityIndex.CalculateAci(amplitudeSpectrogram);
// iii: CALCULATE the H(t) or Temporal ENTROPY Spectrum and then reverse the values i.e. calculate 1-Ht for energy concentration
double[] temporalEntropySpectrum = AcousticEntropy.CalculateTemporalEntropySpectrum(amplitudeSpectrogram);
for (int i = 0; i < temporalEntropySpectrum.Length; i++)
{
temporalEntropySpectrum[i] = 1 - temporalEntropySpectrum[i];
}
spectralIndices.ENT = temporalEntropySpectrum;
// (C) ################################## EXTRACT SPECTRAL INDICES FROM THE DECIBEL SPECTROGRAM ##################################
// i: Convert amplitude spectrogram to decibels and calculate the dB background noise profile
double[,] decibelSpectrogram = MFCCStuff.DecibelSpectra(dspOutput1.AmplitudeSpectrogram, dspOutput1.WindowPower, sampleRate, epsilon);
double[] spectralDecibelBgn = NoiseProfile.CalculateBackgroundNoise(decibelSpectrogram);
spectralIndices.BGN = spectralDecibelBgn;
// ii: Calculate the noise reduced decibel spectrogram derived from segment recording.
// REUSE the var decibelSpectrogram but this time using dspOutput1.
decibelSpectrogram = MFCCStuff.DecibelSpectra(dspOutput1.AmplitudeSpectrogram, dspOutput1.WindowPower, sampleRate, epsilon);
decibelSpectrogram = SNR.TruncateBgNoiseFromSpectrogram(decibelSpectrogram, spectralDecibelBgn);
decibelSpectrogram = SNR.RemoveNeighbourhoodBackgroundNoise(decibelSpectrogram, nhThreshold: 2.0);
// iii: CALCULATE noise reduced AVERAGE DECIBEL SPECTRUM
spectralIndices.PMN = SpectrogramTools.CalculateAvgDecibelSpectrumFromDecibelSpectrogram(decibelSpectrogram);
// ######################################################################################################################################################
// iv: CALCULATE SPECTRAL COVER. NOTE: at this point, decibelSpectrogram is noise reduced. All values >= 0.0
// FreqBinWidth can be accessed, if required, through dspOutput1.FreqBinWidth
// dB THRESHOLD for calculating spectral coverage
double dBThreshold = ActivityAndCover.DefaultActivityThresholdDb;
// Calculate lower and upper boundary bin ids.
// Boundary between low & mid frequency bands is to avoid low freq bins containing anthropogenic noise. These biased index values away from bio-phony.
int midFreqBound = config.MidFreqBound;
int lowFreqBound = config.LowFreqBound;
int lowerBinBound = (int)Math.Ceiling(lowFreqBound / dspOutput1.FreqBinWidth);
int middleBinBound = (int)Math.Ceiling(midFreqBound / dspOutput1.FreqBinWidth);
var spActivity = ActivityAndCover.CalculateSpectralEvents(decibelSpectrogram, dBThreshold, frameStepTimeSpan, lowerBinBound, middleBinBound);
//spectralIndices.CVR = spActivity.CoverSpectrum;
spectralIndices.EVN = spActivity.EventSpectrum;
///////result.TrackScores = null;
///////return result;
return(spectralIndices);
} // end calculation of Six Spectral Indices