diff --git a/src/AnalysisPrograms/Create4Sonograms.cs b/src/AnalysisPrograms/Create4Sonograms.cs index 03c60ec4d..fe85eae73 100644 --- a/src/AnalysisPrograms/Create4Sonograms.cs +++ b/src/AnalysisPrograms/Create4Sonograms.cs @@ -112,7 +112,7 @@ public static void Main(Arguments arguments) var recording = new AudioRecording(fiOutputSegment.FullName); - // EXTRACT ENVELOPE and SPECTROGRAM + // EXTRACT ENVELOPE and SPECTROGRAM// This call uses the default FFT window. var dspOutput = DSP_Frames.ExtractEnvelopeAndFfts(recording, frameSize, windowOverlap); // average absolute value over the minute recording diff --git a/src/AnalysisPrograms/SnrAnalysis.cs b/src/AnalysisPrograms/SnrAnalysis.cs index 4016871d6..e97d695ae 100644 --- a/src/AnalysisPrograms/SnrAnalysis.cs +++ b/src/AnalysisPrograms/SnrAnalysis.cs @@ -114,6 +114,7 @@ public static void Execute(Arguments arguments) int frameCount = signalLength / stepSize; // (B) ################################## EXTRACT ENVELOPE and SPECTROGRAM ################################## + // Calling this method will set the default FFT window. var dspOutput = DSP_Frames.ExtractEnvelopeAndFfts( recording, sonoConfig.WindowSize, diff --git a/src/AudioAnalysisTools/DSP/DSP_Frames.cs b/src/AudioAnalysisTools/DSP/DSP_Frames.cs index 3b3d575e6..66ba41ae6 100644 --- a/src/AudioAnalysisTools/DSP/DSP_Frames.cs +++ b/src/AudioAnalysisTools/DSP/DSP_Frames.cs @@ -133,22 +133,31 @@ public static int FrameStep(int windowSize, double windowOverlap) return frames; } + /// + /// Calling this method will set default FFT window if windowName is null. + /// Otherwise sets the FFT window specified in the config file. + /// public static EnvelopeAndFft ExtractEnvelopeAndFfts(AudioRecording recording, int frameSize, double overlap, string windowName = null) { int frameStep = (int)(frameSize * (1 - overlap)); return ExtractEnvelopeAndAmplSpectrogram(recording.WavReader.Samples, recording.SampleRate, recording.Epsilon, frameSize, frameStep, windowName); } + /// + /// Calling this method sets the default FFT window, currently HANNING - see FFT.cs line 22. + /// public static EnvelopeAndFft ExtractEnvelopeAndFfts(AudioRecording recording, int frameSize, int frameStep) { - string windowName = FFT.KeyHammingWindow; - return ExtractEnvelopeAndAmplSpectrogram(recording.WavReader.Samples, recording.SampleRate, recording.Epsilon, frameSize, frameStep, windowName); + return ExtractEnvelopeAndAmplSpectrogram(recording.WavReader.Samples, recording.SampleRate, recording.Epsilon, frameSize, frameStep, FFT.DefaultFftWindow); } + /// + /// Calling this method sets the default FFT window, currently HANNING - see FFT.cs line 22. + /// public static EnvelopeAndFft ExtractEnvelopeAndAmplSpectrogram(double[] signal, int sampleRate, double epsilon, int frameSize, double overlap) { int frameStep = (int)(frameSize * (1 - overlap)); - return ExtractEnvelopeAndAmplSpectrogram(signal, sampleRate, epsilon, frameSize, frameStep, FFT.KeyHammingWindow); + return ExtractEnvelopeAndAmplSpectrogram(signal, sampleRate, epsilon, frameSize, frameStep, FFT.DefaultFftWindow); } /// @@ -196,7 +205,7 @@ public static EnvelopeAndFft ExtractEnvelopeAndAmplSpectrogram( // set up the FFT parameters if (windowName == null) { - windowName = FFT.KeyHammingWindow; + windowName = FFT.DefaultFftWindow; } FFT.WindowFunc w = FFT.GetWindowFunction(windowName); diff --git a/src/TowseyLibrary/FFT.cs b/src/TowseyLibrary/FFT.cs index 01de9fe37..9862c1b81 100644 --- a/src/TowseyLibrary/FFT.cs +++ b/src/TowseyLibrary/FFT.cs @@ -19,6 +19,7 @@ public sealed class FFT public const string KeyNoWindow = "NONE"; public const string KeyHammingWindow = "HAMMING"; public const string KeyHanningWindow = "HANNING"; + public const string DefaultFftWindow = KeyHanningWindow; public delegate double WindowFunc(int n, int N); @@ -338,9 +339,13 @@ private static double lrw(double a0, double a1, double a2, double a3, int n, int return 1.0 - (1.93 * c1) + (1.29 * c2) - (0.388 * c3) + (0.032 * c4); }; + /// + /// Returns an FFT window function given the name of the window type. + /// + /// FFT window name. + /// FFT.WindowFunc. public static WindowFunc GetWindowFunction(string name) { - //FFT.WindowFunc windowFnc; if (name.StartsWith(KeyHammingWindow)) { return Hamming; diff --git a/tests/Acoustics.Test/AudioAnalysisTools/EventStatistics/EventStatisticsCalculateTests.cs b/tests/Acoustics.Test/AudioAnalysisTools/EventStatistics/EventStatisticsCalculateTests.cs index 2bfe4d817..931f68e27 100644 --- a/tests/Acoustics.Test/AudioAnalysisTools/EventStatistics/EventStatisticsCalculateTests.cs +++ b/tests/Acoustics.Test/AudioAnalysisTools/EventStatistics/EventStatisticsCalculateTests.cs @@ -59,9 +59,9 @@ public void TestCalculateEventStatistics() LoggedConsole.WriteLine($"Stats: DominantFrequency= {stats.DominantFrequency}"); Assert.AreEqual(0.0, stats.TemporalEnergyDistribution, 1E-4); - Assert.AreEqual(0.6062, stats.SpectralEnergyDistribution, 1E-4); - Assert.AreEqual(6687, stats.SpectralCentroid); - Assert.AreEqual(8003, stats.DominantFrequency); + Assert.AreEqual(0.61647, stats.SpectralEnergyDistribution, 1E-4); + Assert.AreEqual(6011, stats.SpectralCentroid); + Assert.AreEqual(3998, stats.DominantFrequency); Assert.AreEqual(1500, stats.LowFrequencyHertz); Assert.AreEqual(8500, stats.HighFrequencyHertz); diff --git a/tests/Acoustics.Test/AudioAnalysisTools/Indices/ClusterIndexTest.cs b/tests/Acoustics.Test/AudioAnalysisTools/Indices/ClusterIndexTest.cs index 58e409c04..2f879f465 100644 --- a/tests/Acoustics.Test/AudioAnalysisTools/Indices/ClusterIndexTest.cs +++ b/tests/Acoustics.Test/AudioAnalysisTools/Indices/ClusterIndexTest.cs @@ -73,10 +73,10 @@ public void TestBinaryClusteringOfSpectra() var clusterSpectrum = SpectralClustering.RestoreFullLengthSpectrum(clusterInfo.ClusterSpectrum, freqBinCount, lowerBinBound); // test the cluster count - also called spectral diversity in some papers - Assert.AreEqual(clusterInfo.ClusterCount, 17); + Assert.AreEqual(clusterInfo.ClusterCount, 19); // test the trigram count - another way of thinking about spectral change - Assert.AreEqual(clusterInfo.TriGramUniqueCount, 342); + Assert.AreEqual(clusterInfo.TriGramUniqueCount, 436); // test what used to be the CLS spectral index. Sum of the rows of the weight vectors. var expectedSpectrumFile = PathHelper.ResolveAsset("BinaryClustering", "clusterSpectrum.bin"); diff --git a/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs b/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs index f6e02e4ec..0c9d733fe 100644 --- a/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs +++ b/tests/Acoustics.Test/AudioAnalysisTools/Indices/IndexCalculateTest.cs @@ -79,27 +79,27 @@ public void TestOfSummaryIndices() var summaryIndices = results.SummaryIndexValues; - Assert.AreEqual(0.6793287, summaryIndices.AcousticComplexity, AllowedDelta); + Assert.AreEqual(0.689085, summaryIndices.AcousticComplexity, AllowedDelta); Assert.AreEqual(0.484520, summaryIndices.Activity, AllowedDelta); Assert.AreEqual(-30.946519, summaryIndices.AvgSignalAmplitude, AllowedDelta); Assert.AreEqual(11.533420, summaryIndices.AvgSnrOfActiveFrames, AllowedDelta); Assert.AreEqual(-39.740775, summaryIndices.BackgroundNoise, AllowedDelta); - Assert.AreEqual(21, summaryIndices.ClusterCount); - Assert.AreEqual(0.153191, summaryIndices.EntropyOfAverageSpectrum, AllowedDelta); - Assert.AreEqual(0.301929, summaryIndices.EntropyOfCoVSpectrum, AllowedDelta); - Assert.AreEqual(0.260999, summaryIndices.EntropyOfPeaksSpectrum, AllowedDelta); - Assert.AreEqual(0.522080, summaryIndices.EntropyOfVarianceSpectrum, AllowedDelta); + Assert.AreEqual(23, summaryIndices.ClusterCount); + Assert.AreEqual(0.153642, summaryIndices.EntropyOfAverageSpectrum, AllowedDelta); + Assert.AreEqual(0.299602, summaryIndices.EntropyOfCoVSpectrum, AllowedDelta); + Assert.AreEqual(0.264981, summaryIndices.EntropyOfPeaksSpectrum, AllowedDelta); + Assert.AreEqual(0.522530, summaryIndices.EntropyOfVarianceSpectrum, AllowedDelta); Assert.AreEqual(2.0, summaryIndices.EventsPerSecond, AllowedDelta); - Assert.AreEqual(0.467151, summaryIndices.SpectralCentroid, AllowedDelta); - Assert.AreEqual(0.140306, summaryIndices.HighFreqCover, AllowedDelta); - Assert.AreEqual(0.137873, summaryIndices.MidFreqCover, AllowedDelta); - Assert.AreEqual(0.055341, summaryIndices.LowFreqCover, AllowedDelta); - Assert.AreEqual(0.957433, summaryIndices.Ndsi, AllowedDelta); + Assert.AreEqual(0.462917, summaryIndices.SpectralCentroid, AllowedDelta); + Assert.AreEqual(0.148697, summaryIndices.HighFreqCover, AllowedDelta); + Assert.AreEqual(0.139938, summaryIndices.MidFreqCover, AllowedDelta); + Assert.AreEqual(0.048843, summaryIndices.LowFreqCover, AllowedDelta); + Assert.AreEqual(0.957532, summaryIndices.Ndsi, AllowedDelta); Assert.AreEqual(27.877206, summaryIndices.Snr, AllowedDelta); - Assert.AreEqual(6.240310, summaryIndices.SptDensity, AllowedDelta); + Assert.AreEqual(6.257752, summaryIndices.SptDensity, AllowedDelta); Assert.AreEqual(0, summaryIndices.ResultStartSeconds); Assert.AreEqual(0.162216, summaryIndices.TemporalEntropy, AllowedDelta); - Assert.AreEqual(401, summaryIndices.ThreeGramCount, AllowedDelta); + Assert.AreEqual(487, summaryIndices.ThreeGramCount, AllowedDelta); } /// @@ -139,7 +139,7 @@ public void TestOfSpectralIndices() // 1:ACI var expectedSpectrumFile = PathHelper.ResolveAsset("Indices", "ACI.bin"); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.ACI); + // Binary.Serialize(expectedSpectrumFile, spectralIndices.ACI); var expectedVector = Binary.Deserialize(expectedSpectrumFile); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.ACI, AllowedDelta); @@ -174,7 +174,7 @@ public void TestOfSpectralIndices() // 6:OSC expectedSpectrumFile = PathHelper.ResolveAsset("Indices", "OSC.bin"); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.OSC); + // Binary.Serialize(expectedSpectrumFile, spectralIndices.OSC); expectedVector = Binary.Deserialize(expectedSpectrumFile); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.OSC, AllowedDelta); @@ -263,13 +263,13 @@ public void TestOfSpectralIndices_ICD20() var resourcesDir = PathHelper.ResolveAssetPath("Indices"); var expectedSpectrumFile = PathHelper.ResolveAsset("Indices", "BGN_ICD20.bin"); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.BGN); + // Binary.Serialize(expectedSpectrumFile, spectralIndices.BGN); var expectedVector = Binary.Deserialize(expectedSpectrumFile); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.BGN, AllowedDelta); expectedSpectrumFile = PathHelper.ResolveAsset("Indices", "CVR_ICD20.bin"); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.CVR); + // Binary.Serialize(expectedSpectrumFile, spectralIndices.CVR); expectedVector = Binary.Deserialize(expectedSpectrumFile); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.CVR, AllowedDelta); @@ -333,12 +333,16 @@ public void TestOfSpectralIndices_Octave() // TEST the BGN SPECTRAL INDEX Assert.AreEqual(256, spectralIndices.BGN.Length); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.BGN); - var expectedVector = Binary.Deserialize(PathHelper.ResolveAsset("Indices", "BGN_OctaveScale.bin")); + var expectedSpectrumFile1 = PathHelper.ResolveAsset("Indices", "BGN_OctaveScale.bin"); + + // Binary.Serialize(expectedSpectrumFile1, spectralIndices.BGN); + var expectedVector = Binary.Deserialize(expectedSpectrumFile1); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.BGN, AllowedDelta); - //Binary.Serialize(expectedSpectrumFile, spectralIndices.CVR); - expectedVector = Binary.Deserialize(PathHelper.ResolveAsset("Indices", "CVR_OctaveScale.bin")); + var expectedSpectrumFile2 = PathHelper.ResolveAsset("Indices", "CVR_OctaveScale.bin"); + + // Binary.Serialize(expectedSpectrumFile2, spectralIndices.CVR); + expectedVector = Binary.Deserialize(expectedSpectrumFile2); CollectionAssert.That.AreEqual(expectedVector, spectralIndices.CVR, AllowedDelta); } } diff --git a/tests/Acoustics.Test/AudioAnalysisTools/Oscillations2014/OscillationTests.cs b/tests/Acoustics.Test/AudioAnalysisTools/Oscillations2014/OscillationTests.cs index da8485b0d..456e97d0f 100644 --- a/tests/Acoustics.Test/AudioAnalysisTools/Oscillations2014/OscillationTests.cs +++ b/tests/Acoustics.Test/AudioAnalysisTools/Oscillations2014/OscillationTests.cs @@ -85,18 +85,13 @@ public void TwoOscillationTests() // construct name of expected matrix osc spectrogram to save file var expectedMatrixFile = PathHelper.ResolveAsset("Oscillations2014", stem + ".Matrix.EXPECTED.csv"); - // SAVE THE OUTPUT if true + // SAVE THE image of oscillation spectrogram if true. // WARNING: this will overwrite fixtures if (false) { - // 1: save image of oscillation spectrogram string imageName = stem + ".EXPECTED.png"; string imagePath = Path.Combine(PathHelper.ResolveAssetPath("Oscillations2014"), imageName); tuple.Item1.Save(imagePath); - - // 2: Save matrix of oscillation data stored in freqOscilMatrix1 - //Csv.WriteMatrixToCsv(expectedMatrixFile, tuple.Item2); - Binary.Serialize(expectedMatrixFile, tuple.Item2); } // Run two tests. Have to deserialise the expected data files @@ -105,6 +100,8 @@ public void TwoOscillationTests() Assert.AreEqual(675, tuple.Item1.Height); // 2. Compare matrix data + // Save matrix in expectedMatrixFile + // Binary.Serialize(expectedMatrixFile, tuple.Item2); var expectedMatrix = Binary.Deserialize(expectedMatrixFile); //TODO Following test fails when using CSV reader because the reader cuts out first line of the matrix @@ -132,35 +129,31 @@ public void SpectralIndexOsc_Test() var threshold = Oscillations2014.DefaultSensitivityThreshold; var spectralIndex = Oscillations2014.GetSpectralIndex_Osc(recordingSegment, frameLength, sampleLength, threshold); - // 3. construct name of spectral index vector - // SAVE THE OUTPUT if true + // 3. construct name of spectral index vector and save as image file + // No need to do tests on this image but it is useful to visualise output // WARNING: this will overwrite fixtures var sourceName = Path.GetFileNameWithoutExtension(sourceRecording.Name); - var stem = sourceName + ".SpectralIndex.OSC"; - var expectedIndexPath = PathHelper.ResolveAsset("Oscillations2014", stem + ".EXPECTED.csv"); if (false) { - // 4. Save spectral index vector to file - //Csv.WriteToCsv(expectedIndexPath, spectralIndex); - //Json.Serialise(expectedIndexPath, spectralIndex); - Binary.Serialize(expectedIndexPath, spectralIndex); - - // 5. Get the vector as image and save as image file - // no need to do tests on this image but it is useful to visualise output var expectedVectorImage = ImageTools.DrawVectorInColour(DataTools.reverseArray(spectralIndex), cellWidth: 10); - var expectedImagePath = PathHelper.ResolveAsset("Oscillations2014", stem + ".png"); + var expectedImagePath = PathHelper.ResolveAsset("Oscillations2014", sourceName + ".SpectralIndex.OSC.png"); expectedVectorImage.Save(expectedImagePath.FullName); } // 6. Get the vector as image and save as image file // no need to do tests on this image but it is useful to compare with expected visual output var currentVectorImage = ImageTools.DrawVectorInColour(DataTools.reverseArray(spectralIndex), cellWidth: 10); - var currentImagePath = Path.Combine(this.outputDirectory.FullName, stem + ".png"); + var currentImagePath = Path.Combine(this.outputDirectory.FullName, sourceName + ".SpectralIndex.OSC.png"); currentVectorImage.Save(currentImagePath); // 7. Run test. Compare vectors // TODO this test fails when using CSV reader because the reader cuts out first element/line of the vector //var expectedVector = (double[])Csv.ReadFromCsv(expectedIndexPath); + var expectedIndexPath = PathHelper.ResolveAsset("Oscillations2014", sourceName + ".SpectralIndex.OSC.EXPECTED.csv"); + + //comment the following line once fixture is saved. + // Binary.Serialize(expectedIndexPath, spectralIndex); + var expectedVector = Binary.Deserialize(expectedIndexPath); CollectionAssert.That.AreEqual(expectedVector, spectralIndex, 0.000001); } diff --git a/tests/Fixtures/BinaryClustering/clusterSpectrum.bin b/tests/Fixtures/BinaryClustering/clusterSpectrum.bin index d0c861a5d..f59c8a9ee 100644 --- a/tests/Fixtures/BinaryClustering/clusterSpectrum.bin +++ b/tests/Fixtures/BinaryClustering/clusterSpectrum.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7b80d03274cf7d5c8ab9d96874232b6483adc65b5179d91e4be9a5685bab13ae +oid sha256:108faa696c3ade02ad9e3ab5b11ea431ebf313e8c16542c613629aab676162fe size 2076 diff --git a/tests/Fixtures/Indices/ACI.bin b/tests/Fixtures/Indices/ACI.bin index 02395d082..1e81810de 100644 --- a/tests/Fixtures/Indices/ACI.bin +++ b/tests/Fixtures/Indices/ACI.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:154506500119ecc9781eaef8b2530e1dbce32f5ebdbad951a3491df8fea0da54 +oid sha256:d7f6bfcc5a90614c0989b21d79be485798cb8320199549e62a1f1315ab1a0e3f size 2076 diff --git a/tests/Fixtures/Indices/BGN.bin b/tests/Fixtures/Indices/BGN.bin index 1b46a4477..978b679ce 100644 --- a/tests/Fixtures/Indices/BGN.bin +++ b/tests/Fixtures/Indices/BGN.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:4bcd87c5191d1a355b2f28fa4ee8164d9be174fed53ae9d6f955f5f5e9c8bbdf +oid sha256:20c781f9aabbd85a3f03091de91fc530e798286436633148fb55feda0b593924 size 2076 diff --git a/tests/Fixtures/Indices/BGN_ICD20.bin b/tests/Fixtures/Indices/BGN_ICD20.bin index aab7f80f2..3cc0dcc92 100644 --- a/tests/Fixtures/Indices/BGN_ICD20.bin +++ b/tests/Fixtures/Indices/BGN_ICD20.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:2ce4c455696ef094744dd5fc3bfe97194aeddd308a288de7606c37b9c5cc2ba8 +oid sha256:d2358ce874c16edeaed512efaa7ddf7a5d22dc01dd561ea3e644d6e256ebcc59 size 2076 diff --git a/tests/Fixtures/Indices/BGN_OctaveScale.bin b/tests/Fixtures/Indices/BGN_OctaveScale.bin index a3cca5db4..7f5ddb82a 100644 --- a/tests/Fixtures/Indices/BGN_OctaveScale.bin +++ b/tests/Fixtures/Indices/BGN_OctaveScale.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:528021ef3170acf932de1b953e302787c0b7cab7e6957b059eee875655d27202 +oid sha256:873fc6aa38bdac712e218eb0867cad930bfc2e8f9600690598bff8b11bc40ecd size 2076 diff --git a/tests/Fixtures/Indices/CVR.bin b/tests/Fixtures/Indices/CVR.bin index bd67606dd..d608b89f0 100644 --- a/tests/Fixtures/Indices/CVR.bin +++ b/tests/Fixtures/Indices/CVR.bin @@ -1,3 +1,3 @@ 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55f32d723..3f7e85655 100644 --- a/tests/Fixtures/Indices/PMN.bin +++ b/tests/Fixtures/Indices/PMN.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:42e246b9814337aab7fde52af2f8c9eadee3d4ce68b48ea2923743de2241b603 +oid sha256:9cbcacd2c758de2826861c41defe79ab02d6bbb500cbc36bac169b68095f9e59 size 2076 diff --git a/tests/Fixtures/Indices/RHZ.bin b/tests/Fixtures/Indices/RHZ.bin index fd9ba793a..db98602aa 100644 --- a/tests/Fixtures/Indices/RHZ.bin +++ b/tests/Fixtures/Indices/RHZ.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:06c22a34dae0d2f11ad8939411977286b038e8b95715b9b0b556f4f95cb12a5f +oid sha256:8e5e52431f0aed668e0b7e92a669f65c3fa283c44f4c0633d7c9b1dc7dbfadfc size 2076 diff --git a/tests/Fixtures/Indices/RNG.bin b/tests/Fixtures/Indices/RNG.bin index 473a638d5..0e74da854 100644 --- a/tests/Fixtures/Indices/RNG.bin +++ b/tests/Fixtures/Indices/RNG.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid 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