} //Analysis()
/// <summary>
/// returns some indices relevant to rain and cicadas from a short (10seconds) chunk of audio
/// </summary>
/// <param name="signal">signal envelope of a 10s chunk of audio</param>
/// <param name="spectrogram">spectrogram of a 10s chunk of audio</param>
/// <param name="lowFreqBound"></param>
/// <param name="midFreqBound"></param>
/// <param name="binWidth"></param>
/// <returns></returns>
public static RainStruct Get10SecondIndices(double[] signal, double[,] spectrogram, int lowFreqBound, int midFreqBound,
TimeSpan frameDuration, double binWidth)
{
// i: FRAME ENERGIES -
double StandardDeviationCount = 0.1;
var results3 = SNR.SubtractBackgroundNoiseFromWaveform_dB(SNR.Signal2Decibels(signal), StandardDeviationCount); //use Lamel et al.
var dBarray = SNR.TruncateNegativeValues2Zero(results3.NoiseReducedSignal);
bool[] activeFrames = new bool[dBarray.Length]; //record frames with activity >= threshold dB above background and count
for (int i = 0; i < dBarray.Length; i++)
{
if (dBarray[i] >= ActivityAndCover.DefaultActivityThresholdDb)
{
activeFrames[i] = true;
}
}
//int activeFrameCount = dBarray.Count((x) => (x >= AcousticIndices.DEFAULT_activityThreshold_dB));
int activeFrameCount = DataTools.CountTrues(activeFrames);
double spikeThreshold = 0.05;
double spikeIndex = CalculateSpikeIndex(signal, spikeThreshold);
//Console.WriteLine("spikeIndex=" + spikeIndex);
//DataTools.writeBarGraph(signal);
RainStruct rainIndices; // struct in which to store all indices
rainIndices.activity = activeFrameCount / (double)dBarray.Length; //fraction of frames having acoustic activity
rainIndices.bgNoise = results3.NoiseMode; //bg noise in dB
rainIndices.snr = results3.Snr; //snr
rainIndices.avSig_dB = 20 * Math.Log10(signal.Average()); //10 times log of amplitude squared
rainIndices.temporalEntropy = DataTools.EntropyNormalised(DataTools.SquareValues(signal)); //ENTROPY of ENERGY ENVELOPE
rainIndices.spikes = spikeIndex;
// ii: calculate the bin id of boundary between mid and low frequency spectrum
int lowBinBound = (int)Math.Ceiling(lowFreqBound / binWidth);
var midbandSpectrogram = MatrixTools.Submatrix(spectrogram, 0, lowBinBound, spectrogram.GetLength(0) - 1, spectrogram.GetLength(1) - 1);
// iii: ENTROPY OF AVERAGE SPECTRUM and VARIANCE SPECTRUM - at this point the spectrogram is still an amplitude spectrogram
var tuple = SpectrogramTools.CalculateAvgSpectrumAndVarianceSpectrumFromAmplitudeSpectrogram(midbandSpectrogram);
rainIndices.spectralEntropy = DataTools.EntropyNormalised(tuple.Item1); //ENTROPY of spectral averages
if (double.IsNaN(rainIndices.spectralEntropy))
{
rainIndices.spectralEntropy = 1.0;
}
// iv: CALCULATE Acoustic Complexity Index on the AMPLITUDE SPECTRUM
var aciArray = AcousticComplexityIndex.CalculateAci(midbandSpectrogram);
rainIndices.ACI = aciArray.Average();
//v: remove background noise from the spectrogram
double spectralBgThreshold = 0.015; // SPECTRAL AMPLITUDE THRESHOLD for smoothing background
//double[] modalValues = SNR.CalculateModalValues(spectrogram); //calculate modal value for each freq bin.
//modalValues = DataTools.filterMovingAverage(modalValues, 7); //smooth the modal profile
//spectrogram = SNR.SubtractBgNoiseFromSpectrogramAndTruncate(spectrogram, modalValues);
//spectrogram = SNR.RemoveNeighbourhoodBackgroundNoise(spectrogram, spectralBgThreshold);
//vi: SPECTROGRAM ANALYSIS - SPECTRAL COVER. NOTE: spectrogram is still a noise reduced amplitude spectrogram
SpectralActivity sa = ActivityAndCover.CalculateSpectralEvents(spectrogram, spectralBgThreshold, frameDuration, lowFreqBound, midFreqBound, binWidth);
rainIndices.lowFreqCover = sa.LowFreqBandCover;
rainIndices.midFreqCover = sa.MidFreqBandCover;
rainIndices.hiFreqCover = sa.HighFreqBandCover;
//double[] coverSpectrum = sa.coverSpectrum;
//double[] eventSpectrum = sa.eventSpectrum;
return(rainIndices);
}
//////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
public static IndexCalculateResult Analysis(
AudioRecording recording,
TimeSpan subsegmentOffsetTimeSpan,
Dictionary <string, IndexProperties> indexProperties,
int sampleRateOfOriginalAudioFile,
TimeSpan segmentStartOffset,
IndexCalculateConfig config,
bool returnSonogramInfo = false)
{
// returnSonogramInfo = true; // if debugging
double epsilon = recording.Epsilon;
int signalLength = recording.WavReader.GetChannel(0).Length;
int sampleRate = recording.WavReader.SampleRate;
var segmentDuration = TimeSpan.FromSeconds(recording.WavReader.Time.TotalSeconds);
var indexCalculationDuration = config.IndexCalculationDurationTimeSpan;
int nyquist = sampleRate / 2;
// Get FRAME parameters for the calculation of Acoustic Indices
//WARNING: DO NOT USE Frame Overlap when calculating acoustic indices.
// It yields ACI, BGN, POW and EVN results that are significantly different from the default.
// I have not had time to check if the difference is meaningful. Best to avoid.
//int frameSize = (int?)config[AnalysisKeys.FrameLength] ?? IndexCalculateConfig.DefaultWindowSize;
int frameSize = config.FrameLength;
int frameStep = frameSize; // that is, windowOverlap = zero
double frameStepDuration = frameStep / (double)sampleRate; // fraction of a second
var frameStepTimeSpan = TimeSpan.FromTicks((long)(frameStepDuration * TimeSpan.TicksPerSecond));
int midFreqBound = config.MidFreqBound;
int lowFreqBound = config.LowFreqBound;
int freqBinCount = frameSize / 2;
// double freqBinWidth = recording.Nyquist / (double)freqBinCount;
// get duration in seconds and sample count and frame count
double subsegmentDurationInSeconds = indexCalculationDuration.TotalSeconds;
int subsegmentSampleCount = (int)(subsegmentDurationInSeconds * sampleRate);
double subsegmentFrameCount = subsegmentSampleCount / (double)frameStep;
subsegmentFrameCount = (int)Math.Ceiling(subsegmentFrameCount);
// In order not to lose the last fractional frame, round up the frame number
// and get the exact number of samples in the integer number of frames.
// Do this because when IndexCalculationDuration = 100ms, the number of frames is only 8.
subsegmentSampleCount = (int)(subsegmentFrameCount * frameStep);
// get start and end samples of the subsegment and noise segment
double localOffsetInSeconds = subsegmentOffsetTimeSpan.TotalSeconds - segmentStartOffset.TotalSeconds;
int startSample = (int)(localOffsetInSeconds * sampleRate);
int endSample = startSample + subsegmentSampleCount - 1;
// Default behaviour: set SUBSEGMENT = total recording
var subsegmentRecording = recording;
// But if the indexCalculationDuration < segmentDuration
if (indexCalculationDuration < segmentDuration)
{
// minimum samples needed to calculate acoustic indices. This value was chosen somewhat arbitrarily.
// It allowes for case where IndexCalculationDuration = 100ms which is approx 8 frames
int minimumViableSampleCount = frameSize * 8;
int availableSignal = signalLength - startSample;
// if (the required audio is beyond recording OR insufficient for analysis) then backtrack.
if (availableSignal < minimumViableSampleCount)
{
// Back-track so we can fill a whole result.
// This is a silent correction, equivalent to having a segment overlap for the last segment.
var oldStart = startSample;
startSample = signalLength - subsegmentSampleCount;
endSample = signalLength;
Logger.Trace(" Backtrack subsegment to fill missing data from imperfect audio cuts because not enough samples available. " + (oldStart - startSample) + " samples overlap.");
}
var subsamples = DataTools.Subarray(recording.WavReader.Samples, startSample, subsegmentSampleCount);
var wr = new Acoustics.Tools.Wav.WavReader(subsamples, 1, 16, sampleRate);
subsegmentRecording = new AudioRecording(wr);
}
// INITIALISE a RESULTS STRUCTURE TO return
// initialize a result object in which to store SummaryIndexValues and SpectralIndexValues etc.
var result = new IndexCalculateResult(freqBinCount, indexProperties, indexCalculationDuration, subsegmentOffsetTimeSpan, config);
SummaryIndexValues summaryIndices = result.SummaryIndexValues;
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>();
// ################################## FINSIHED SET-UP
// ################################## NOW GET THE AMPLITUDE SPECTORGRAMS
// EXTRACT ENVELOPE and SPECTROGRAM FROM SUBSEGMENT
var dspOutput1 = DSP_Frames.ExtractEnvelopeAndFfts(subsegmentRecording, frameSize, frameStep);
// Select band according to min and max bandwidth
int minBand = (int)(dspOutput1.AmplitudeSpectrogram.GetLength(1) * config.MinBandWidth);
int maxBand = (int)(dspOutput1.AmplitudeSpectrogram.GetLength(1) * config.MaxBandWidth) - 1;
dspOutput1.AmplitudeSpectrogram = MatrixTools.Submatrix(
dspOutput1.AmplitudeSpectrogram,
0,
minBand,
dspOutput1.AmplitudeSpectrogram.GetLength(0) - 1,
maxBand);
// TODO: Michael to review whether bandwidth filter should be moved to DSP_Frames??
// Recalculate NyquistBin and FreqBinWidth, because they change with band selection
//dspOutput1.NyquistBin = dspOutput1.AmplitudeSpectrogram.GetLength(1) - 1;
//dspOutput1.FreqBinWidth = sampleRate / (double)dspOutput1.AmplitudeSpectrogram.GetLength(1) / 2;
// Linear or Octave or Mel frequency scale? Set Linear as default.
var freqScale = new FrequencyScale(nyquist: nyquist, frameSize: frameSize, hertzGridInterval: 1000);
var freqScaleType = config.FrequencyScale;
bool octaveScale = freqScaleType == FreqScaleType.Linear125Octaves7Tones28Nyquist32000;
bool melScale = freqScaleType == FreqScaleType.Mel;
if (octaveScale)
{
// only allow one octave scale at the moment - for Jasco marine recordings.
// ASSUME fixed Occtave scale - USEFUL ONLY FOR JASCO 64000sr MARINE RECORDINGS
// If you wish to use other octave scale types then need to put in the config file and and set up recovery here.
freqScale = new FrequencyScale(FreqScaleType.Linear125Octaves7Tones28Nyquist32000);
// Recalculate the spectrogram according to octave scale. This option works only when have high SR recordings.
dspOutput1.AmplitudeSpectrogram = OctaveFreqScale.AmplitudeSpectra(
dspOutput1.AmplitudeSpectrogram,
dspOutput1.WindowPower,
sampleRate,
epsilon,
freqScale);
dspOutput1.NyquistBin = dspOutput1.AmplitudeSpectrogram.GetLength(1) - 1; // ASSUMPTION!!! Nyquist is in top Octave bin - not necessarily true!!
}
else if (melScale)
{
int minFreq = 0;
int maxFreq = recording.Nyquist;
dspOutput1.AmplitudeSpectrogram = MFCCStuff.MelFilterBank(
dspOutput1.AmplitudeSpectrogram,
config.MelScale,
recording.Nyquist,
minFreq,
maxFreq);
dspOutput1.NyquistBin = dspOutput1.AmplitudeSpectrogram.GetLength(1) - 1;
// TODO: This doesn't make any sense, since the frequency width changes for each bin. Probably need to set this to NaN.
// TODO: Whatever uses this value below, should probably be changed to not be depending on it.
dspOutput1.FreqBinWidth = sampleRate / (double)dspOutput1.AmplitudeSpectrogram.GetLength(1) / 2;
}
// NOW EXTRACT SIGNAL FOR BACKGROUND NOISE CALCULATION
// If the index calculation duration >= 30 seconds, then calculate BGN from the existing segment of recording.
bool doSeparateBgnNoiseCalculation = indexCalculationDuration.TotalSeconds + (2 * config.BgNoiseBuffer.TotalSeconds) < segmentDuration.TotalSeconds / 2;
var dspOutput2 = dspOutput1;
if (doSeparateBgnNoiseCalculation)
{
// GET a longer SUBSEGMENT FOR NOISE calculation with 5 sec buffer on either side.
// If the index calculation duration is shorter than 30 seconds, then need to calculate BGN noise from a longer length of recording
// i.e. need to add noiseBuffer either side. Typical noiseBuffer value = 5 seconds
int sampleBuffer = (int)(config.BgNoiseBuffer.TotalSeconds * sampleRate);
var bgnRecording = AudioRecording.GetRecordingSubsegment(recording, startSample, endSample, sampleBuffer);
// EXTRACT ENVELOPE and SPECTROGRAM FROM BACKGROUND NOISE SUBSEGMENT
dspOutput2 = DSP_Frames.ExtractEnvelopeAndFfts(bgnRecording, frameSize, frameStep);
// If necessary, recalculate the spectrogram according to octave scale. This option works only when have high SR recordings.
if (octaveScale)
{
// ASSUME fixed Occtave scale - USEFUL ONLY FOR JASCO 64000sr MARINE RECORDINGS
// If you wish to use other octave scale types then need to put in the config file and and set up recovery here.
dspOutput2.AmplitudeSpectrogram = OctaveFreqScale.AmplitudeSpectra(
dspOutput2.AmplitudeSpectrogram,
dspOutput2.WindowPower,
sampleRate,
epsilon,
freqScale);
dspOutput2.NyquistBin = dspOutput2.AmplitudeSpectrogram.GetLength(1) - 1; // ASSUMPTION!!! Nyquist is in top Octave bin - not necessarily true!!
}
}
// ###################################### BEGIN CALCULATION OF INDICES ##################################
// (A) ################################## EXTRACT SUMMARY INDICES FROM THE SIGNAL WAVEFORM ##################################
// average absolute value over the minute recording - not useful
// double[] avAbsolute = dspOutput1.Average;
double[] signalEnvelope = dspOutput1.Envelope;
double avgSignalEnvelope = signalEnvelope.Average();
// 10 times log of amplitude squared
summaryIndices.AvgSignalAmplitude = 20 * Math.Log10(avgSignalEnvelope);
// Deal with case where the signal waveform is continuous flat with values < 0.001. Has happened!!
// Although signal appears zero, this condition is required.
if (avgSignalEnvelope < 0.0001)
{
Logger.Debug("Segment skipped because avSignalEnvelope is < 0.001!");
summaryIndices.ZeroSignal = 1.0;
return(result);
}
// i. Check for clipping and high amplitude rates per second
summaryIndices.HighAmplitudeIndex = dspOutput1.HighAmplitudeCount / subsegmentDurationInSeconds;
summaryIndices.ClippingIndex = dspOutput1.ClipCount / subsegmentDurationInSeconds;
// ii. Calculate bg noise in dB
// Convert signal envelope to dB and subtract background noise. Default noise SD to calculate threshold = ZERO
double signalBgn = NoiseRemovalModal.CalculateBackgroundNoise(dspOutput2.Envelope);
summaryIndices.BackgroundNoise = signalBgn;
// iii: FRAME ENERGIES - convert signal to decibels and subtract background noise.
double[] dBEnvelope = SNR.Signal2Decibels(dspOutput1.Envelope);
double[] dBEnvelopeSansNoise = SNR.SubtractAndTruncate2Zero(dBEnvelope, signalBgn);
// iv: ACTIVITY for NOISE REDUCED SIGNAL ENVELOPE
// Calculate fraction of frames having acoustic activity
var activity = ActivityAndCover.CalculateActivity(dBEnvelopeSansNoise, frameStepTimeSpan);
summaryIndices.Activity = activity.FractionOfActiveFrames;
// v. average number of events per second whose duration > one frame
// average event duration in milliseconds - no longer calculated
//summaryIndices.AvgEventDuration = activity.avEventDuration;
summaryIndices.EventsPerSecond = activity.EventCount / subsegmentDurationInSeconds;
// vi. Calculate SNR and active frames SNR
summaryIndices.Snr = dBEnvelopeSansNoise.Max();
summaryIndices.AvgSnrOfActiveFrames = activity.ActiveAvDb;
// vii. ENTROPY of ENERGY ENVELOPE -- 1-Ht because want measure of concentration of acoustic energy.
double entropy = DataTools.EntropyNormalised(DataTools.SquareValues(signalEnvelope));
summaryIndices.TemporalEntropy = 1 - entropy;
// Note that the spectrogram has had the DC bin removed. i.e. has only 256 columns.
double[,] amplitudeSpectrogram = dspOutput1.AmplitudeSpectrogram; // get amplitude spectrogram.
// CALCULATE various NDSI (Normalised difference soundscape Index) FROM THE AMPLITUDE SPECTROGRAM
// These options proved to be highly correlated. Therefore only use tuple.Item 1 which derived from Power Spectral Density.
var tuple3 = SpectrogramTools.CalculateAvgSpectrumAndVarianceSpectrumFromAmplitudeSpectrogram(amplitudeSpectrogram);
summaryIndices.Ndsi = SpectrogramTools.CalculateNdsi(tuple3.Item1, sampleRate, 1000, 2000, 8000);
// (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(subsegmentRecording, frameLength, sampleLength, sensitivity);
// double length of the vector because want to work with 256 element vector for LDFC purposes
spectralIndices.OSC = DataTools.VectorDoubleLengthByAverageInterpolation(spectralIndexShort);
// (C) ################################## EXTRACT SPECTRAL INDICES FROM THE AMPLITUDE SPECTROGRAM ##################################
// i: CALCULATE SPECTRUM OF THE SUM OF FREQ BIN AMPLITUDES - used for later calculation of ACI
spectralIndices.SUM = MatrixTools.SumColumns(amplitudeSpectrogram);
// 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 biophony.
// Boundary of upper bird-band is to avoid high freq artefacts due to mp3.
int lowerBinBound = (int)Math.Ceiling(lowFreqBound / dspOutput1.FreqBinWidth);
int middleBinBound = (int)Math.Ceiling(midFreqBound / dspOutput1.FreqBinWidth);
// calculate number of freq bins in the bird-band.
int midBandBinCount = middleBinBound - lowerBinBound + 1;
if (octaveScale)
{
// the above frequency bin bounds do not apply with octave scale. Need to recalculate them suitable for Octave scale recording.
lowFreqBound = freqScale.LinearBound;
lowerBinBound = freqScale.GetBinIdForHerzValue(lowFreqBound);
midFreqBound = 8000; // This value appears suitable for Jasco Marine recordings. Not much happens above 8kHz.
//middleBinBound = freqScale.GetBinIdForHerzValue(midFreqBound);
middleBinBound = freqScale.GetBinIdInReducedSpectrogramForHerzValue(midFreqBound);
midBandBinCount = middleBinBound - lowerBinBound + 1;
}
// 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 upsampling has been done
if (dspOutput1.NyquistFreq > originalNyquist)
{
dspOutput1.NyquistFreq = originalNyquist;
dspOutput1.NyquistBin = (int)Math.Floor(originalNyquist / dspOutput1.FreqBinWidth); // note that binwidth does not change
}
// ii: CALCULATE THE ACOUSTIC COMPLEXITY INDEX
spectralIndices.DIF = AcousticComplexityIndex.SumOfAmplitudeDifferences(amplitudeSpectrogram);
double[] aciSpectrum = AcousticComplexityIndex.CalculateAci(amplitudeSpectrogram);
spectralIndices.ACI = aciSpectrum;
// remove low freq band of ACI spectrum and store average ACI value
double[] reducedAciSpectrum = DataTools.Subarray(aciSpectrum, lowerBinBound, midBandBinCount);
summaryIndices.AcousticComplexity = reducedAciSpectrum.Average();
// 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;
// iv: remove background noise from the amplitude spectrogram
// First calculate the noise profile from the amplitude sepctrogram
double[] spectralAmplitudeBgn = NoiseProfile.CalculateBackgroundNoise(dspOutput2.AmplitudeSpectrogram);
amplitudeSpectrogram = SNR.TruncateBgNoiseFromSpectrogram(amplitudeSpectrogram, spectralAmplitudeBgn);
// AMPLITUDE THRESHOLD for smoothing background, nhThreshold, assumes background noise ranges around -40dB.
// This value corresponds to approximately 6dB above backgorund.
amplitudeSpectrogram = SNR.RemoveNeighbourhoodBackgroundNoise(amplitudeSpectrogram, nhThreshold: 0.015);
////ImageTools.DrawMatrix(spectrogramData, @"C:\SensorNetworks\WavFiles\Crows\image.png", false);
////DataTools.writeBarGraph(modalValues);
result.AmplitudeSpectrogram = amplitudeSpectrogram;
// v: ENTROPY OF AVERAGE SPECTRUM & VARIANCE SPECTRUM - at this point the spectrogram is a noise reduced amplitude spectrogram
var tuple = AcousticEntropy.CalculateSpectralEntropies(amplitudeSpectrogram, lowerBinBound, midBandBinCount);
// ENTROPY of spectral averages - Reverse the values i.e. calculate 1-Hs and 1-Hv, and 1-Hcov for energy concentration
summaryIndices.EntropyOfAverageSpectrum = 1 - tuple.Item1;
// ENTROPY of spectrum of Variance values
summaryIndices.EntropyOfVarianceSpectrum = 1 - tuple.Item2;
// ENTROPY of spectrum of Coefficient of Variation values
summaryIndices.EntropyOfCoVSpectrum = 1 - tuple.Item3;
// vi: ENTROPY OF DISTRIBUTION of maximum SPECTRAL PEAKS.
// First extract High band SPECTROGRAM which is now noise reduced
double entropyOfPeaksSpectrum = AcousticEntropy.CalculateEntropyOfSpectralPeaks(amplitudeSpectrogram, lowerBinBound, middleBinBound);
summaryIndices.EntropyOfPeaksSpectrum = 1 - entropyOfPeaksSpectrum;
// ######################################################################################################################################################
// (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(dspOutput2.AmplitudeSpectrogram, dspOutput2.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
double dBThreshold = ActivityAndCover.DefaultActivityThresholdDb; // dB THRESHOLD for calculating spectral coverage
var spActivity = ActivityAndCover.CalculateSpectralEvents(deciBelSpectrogram, dBThreshold, frameStepTimeSpan, lowerBinBound, middleBinBound);
spectralIndices.CVR = spActivity.CoverSpectrum;
spectralIndices.EVN = spActivity.EventSpectrum;
summaryIndices.HighFreqCover = spActivity.HighFreqBandCover;
summaryIndices.MidFreqCover = spActivity.MidFreqBandCover;
summaryIndices.LowFreqCover = spActivity.LowFreqBandCover;
// ######################################################################################################################################################
// v: CALCULATE SPECTRAL PEAK TRACKS and RIDGE indices.
// NOTE: at this point, the var decibelSpectrogram is noise reduced. i.e. all its values >= 0.0
// Detecting ridges or spectral peak tracks requires using a 5x5 mask which has edge effects.
// This becomes significant if we have a short indexCalculationDuration.
// Consequently if the indexCalculationDuration < 10 seconds then we revert back to the recording and cut out a recording segment that includes
// a buffer for edge effects. In most cases however, we can just use the decibel spectrogram already calculated and ignore the edge effects.
double peakThreshold = 6.0; //dB
SpectralPeakTracks sptInfo;
if (indexCalculationDuration.TotalSeconds < 10.0)
{
// calculate a new decibel spectrogram
sptInfo = SpectralPeakTracks.CalculateSpectralPeakTracks(recording, startSample, endSample, frameSize, octaveScale, peakThreshold);
}
else
{
// use existing decibel spectrogram
sptInfo = new SpectralPeakTracks(deciBelSpectrogram, peakThreshold);
}
spectralIndices.SPT = sptInfo.SptSpectrum;
spectralIndices.RHZ = sptInfo.RhzSpectrum;
spectralIndices.RVT = sptInfo.RvtSpectrum;
spectralIndices.RPS = sptInfo.RpsSpectrum;
spectralIndices.RNG = sptInfo.RngSpectrum;
summaryIndices.SptDensity = sptInfo.TrackDensity;
// these are two other indices that I tried but they do not seem to add anything of interest.
//summaryIndices.AvgSptDuration = sptInfo.AvTrackDuration;
//summaryIndices.SptPerSecond = sptInfo.TotalTrackCount / subsegmentSecondsDuration;
// ######################################################################################################################################################
// vi: CLUSTERING - FIRST DETERMINE IF IT IS WORTH DOING
// return if (activeFrameCount too small || eventCount == 0 || short index calc duration) because no point doing clustering
if (activity.ActiveFrameCount <= 2 || Math.Abs(activity.EventCount) < 0.01 || indexCalculationDuration.TotalSeconds < 15)
{
// IN ADDITION return if indexCalculationDuration < 15 seconds because no point doing clustering on short time segment
// NOTE: Activity was calculated with 3dB threshold AFTER backgroundnoise removal.
//summaryIndices.AvgClusterDuration = TimeSpan.Zero;
summaryIndices.ClusterCount = 0;
summaryIndices.ThreeGramCount = 0;
return(result);
}
// YES WE WILL DO CLUSTERING! to determine cluster count (spectral diversity) and spectral persistence.
// Only use midband decibel SPECTRUM. In June 2016, the mid-band (i.e. the bird-band) was set to lowerBound=1000Hz, upperBound=8000hz.
// Actually do clustering of binary spectra. Must first threshold
double binaryThreshold = SpectralClustering.DefaultBinaryThresholdInDecibels;
var midBandSpectrogram = MatrixTools.Submatrix(deciBelSpectrogram, 0, lowerBinBound, deciBelSpectrogram.GetLength(0) - 1, middleBinBound);
var clusterInfo = SpectralClustering.ClusterTheSpectra(midBandSpectrogram, lowerBinBound, middleBinBound, binaryThreshold);
// Store two summary index values from cluster info
summaryIndices.ClusterCount = clusterInfo.ClusterCount;
summaryIndices.ThreeGramCount = clusterInfo.TriGramUniqueCount;
// As of May 2017, no longer store clustering results superimposed on spectrogram.
// If you want to see this, then call the TEST methods in class SpectralClustering.cs.
// #######################################################################################################################################################
// vii: set up other info to return
var freqPeaks = SpectralPeakTracks.ConvertSpectralPeaksToNormalisedArray(deciBelSpectrogram);
var scores = new List <Plot>
{
new Plot("Decibels", DataTools.normalise(dBEnvelopeSansNoise), ActivityAndCover.DefaultActivityThresholdDb),
new Plot("Active Frames", DataTools.Bool2Binary(activity.ActiveFrames), 0.0),
new Plot("Max Frequency", freqPeaks, 0.0), // relative location of freq maxima in spectra
};
result.Hits = sptInfo.Peaks;
result.TrackScores = scores;
return(result);
} // end Calculation of Summary and Spectral Indices