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Attempt to implement pulase train detection
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| // -------------------------------------------------------------------------------------------------------------------- | ||
| // <copyright file="PulseTrain.cs" company="QutEcoacoustics"> | ||
| // All code in this file and all associated files are the copyright and property of the QUT Ecoacoustics Research Group (formerly MQUTeR, and formerly QUT Bioacoustics Research Group). | ||
| // </copyright> | ||
| // <summary> | ||
| // This class contains methods to recognise pulse trains. | ||
| // It is an alternative to using the Oscillations class. | ||
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| using System; | ||
| using System.Collections.Generic; | ||
| using System.Linq; | ||
| using System.Text; | ||
| using System.Threading.Tasks; | ||
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| namespace TowseyLibrary | ||
| { | ||
| using Acoustics.Shared.ConfigFile; | ||
| using MathNet.Numerics.LinearAlgebra.Solvers; | ||
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| public static class PulseTrain | ||
| { | ||
| /// <summary> | ||
| /// This method creates a template to recognise two pulses that are possibly part of a pulse train. | ||
| /// The template is designed to detect pulse trains of at least 2 pulses! | ||
| /// The template is bounded either end by silence and then a pulse. i.e. .:|:. ... .:|:. where .=zero or a negative residual value, := 0.5 and |= 1.0. | ||
| /// Any number of residual values may separate the pulses at either end. In this method, templates are created with 6 non-zero values and the remainder are negative. | ||
| /// The sum of the positive values = 4.0. | ||
| /// The sum of the values in the template should = zero. | ||
| /// Designed this way, the minimum pulse length is about 4 or 5 and the minimum template length is about 10; | ||
| /// </summary> | ||
| /// <param name="pulseLength">length or number of frames between two pulses.</param> | ||
| /// <returns>the template.</returns> | ||
| public static double[] GetPulseTrainTemplate(int pulseLength) | ||
| { | ||
| int templateLength = pulseLength + 5; | ||
| double residual = 4 / (double)(templateLength - 6); | ||
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| var template = new double[templateLength]; | ||
| template[0] = -residual; | ||
| template[1] = 0.5; | ||
| template[2] = 1.0; | ||
| template[3] = 0.5; | ||
| for (int i = 4; i < templateLength - 4; i++) | ||
| { | ||
| template[i] = -residual; | ||
| } | ||
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| template[templateLength - 4] = 0.5; | ||
| template[templateLength - 3] = 1.0; | ||
| template[templateLength - 2] = 0.5; | ||
| template[templateLength - 1] = -residual; | ||
| template = DataTools.normalise2UnitLength(template); | ||
| return template; | ||
| } | ||
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| /// <summary> | ||
| /// Only three pulses included in the single template output by this method. | ||
| /// Will generalise if it seems worthwhile. | ||
| /// </summary> | ||
| public static double[] GetPulseTrainTemplate(int pulseLength, int pulseCount) | ||
| { | ||
| int templateLength = (pulseLength * pulseCount) + 5; | ||
| var template = new double[templateLength]; | ||
| int templateHalfLength = templateLength / 2; | ||
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| for (int i = 0; i < templateLength; i++) | ||
| { | ||
| template[i] = -1.0; | ||
| } | ||
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| template[1] = 0.3; | ||
| template[2] = 1.0; | ||
| template[3] = 0.3; | ||
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| template[templateHalfLength - 1] = 0.3; | ||
| template[templateHalfLength] = 1.0; | ||
| template[templateHalfLength + 1] = 0.3; | ||
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| template[templateLength - 4] = 0.3; | ||
| template[templateLength - 3] = 1.0; | ||
| template[templateLength - 2] = 0.3; | ||
| //template = DataTools.normalise2UnitLength(template); | ||
| return template; | ||
| } | ||
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| /// <summary> | ||
| /// returns the length of a pulse interval in frames given pulses and frame rates in seconds. | ||
| /// </summary> | ||
| /// <param name="pulsesPerSecond">number of pulses per second.</param> | ||
| /// <param name="framesPerSecond">frames per second - i.e. assuming the application is applied to a sequence of spectral frames.</param> | ||
| /// <returns>the template.</returns> | ||
| public static double[] GetPulseTrainTemplate(double pulsesPerSecond, double framesPerSecond) | ||
| { | ||
| int frameCount = (int)Math.Round(framesPerSecond / pulsesPerSecond); | ||
| return GetPulseTrainTemplate(frameCount); | ||
| } | ||
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| public static double[] GetPulseTrainScore(double[] signal, double pulsesPerSecond, double framesPerSecond, double thresholdValue) | ||
| { | ||
| int pulseCount = 2; | ||
| int frameCount = (int)Math.Round(framesPerSecond / pulsesPerSecond); | ||
| var templates = new List<double[]> | ||
| { | ||
| GetPulseTrainTemplate(frameCount, pulseCount), | ||
| GetPulseTrainTemplate(frameCount - 1, pulseCount), | ||
| GetPulseTrainTemplate(frameCount + 1, pulseCount), | ||
| }; | ||
| int signalLength = signal.Length; | ||
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| var scores = new double[signalLength]; | ||
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| for (int i = 2; i < signalLength - templates[2].Length; i++) | ||
| { | ||
| // skip if value is below threshold | ||
| if (signal[i] < thresholdValue) | ||
| { | ||
| continue; | ||
| } | ||
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| // skip if value is not maximum | ||
| if (signal[i] < signal[i - 1] || signal[i] < signal[i + 1]) | ||
| { | ||
| continue; | ||
| } | ||
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| // get Cosine similarity for each of three templates. | ||
| var templateScores = new double[3]; | ||
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| // get the local nh of signal for template 0 and get score | ||
| var nh = DataTools.Subarray(signal, i, templates[0].Length); | ||
| nh = DataTools.normalise2UnitLength(nh); | ||
| templateScores[0] = DataTools.DotProduct(nh, templates[0]); | ||
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| // get the local nh of signal for template 1 | ||
| nh = DataTools.Subarray(signal, i, templates[1].Length); | ||
| nh = DataTools.normalise2UnitLength(nh); | ||
| templateScores[1] = DataTools.DotProduct(nh, templates[1]); | ||
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| // get the local nh of signal for template 2 | ||
| nh = DataTools.Subarray(signal, i, templates[2].Length); | ||
| nh = DataTools.normalise2UnitLength(nh); | ||
| templateScores[2] = DataTools.DotProduct(nh, templates[2]); | ||
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| double maxScore = templateScores.Max(); | ||
| if (maxScore > 0.0) | ||
| { | ||
| for (int j = 0; j < templates[0].Length - 1; j++) | ||
| { | ||
| if (maxScore > scores[i + j]) | ||
| { | ||
| scores[i + j] = maxScore; | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| return scores; | ||
| } | ||
| } | ||
| } |
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