Rescaling of plot graphs for generic recogniser

Fixes #469

Update MultiRecognizer.cs

Issue #469 Minor changes. Except change the FFT window from Hamming to Hanning.

Update DataToolsTests.cs

Issue #469 Add a new test method to check that the scaling of image plots is working.

Update GenericRecognizerTests.cs

Issue #469 Remove hard-coded path.

Update GenericRecognizer.cs

Issue #469 Add in code to rescale the plots to fit the current spectrogram.

Changed the signature to SpectrogramTools.GetSonogramPlusCharts()

Issue #469 Changed the signature to SpectrogramTools.GetSonogramPlusCharts() so that it also includes the title of the spectrogram. THis affected these 6 methods.

Rescaling of the plots happens here.

Issue #469 This is ensures that all plots are the same length as the last spectrogram.

Update SpectrogramTools.cs

Issue #469  Fix the drawing of spectrograms.

Update BlobEvent.cs

Issue #469 The plot was being added twice for Blob events. Removed one of them.

Update OscillationEvent.cs

Issue #469
1: Added the Periodicity Property to the Oscillation Event class.
2: Fixed the Draw() method for Oscillation events. The events were not drawing.
3: Added a method to trim Oscillation events using the decibel values as a guide to where the true bounds should be.

Update Oscillations2019.cs

Issue #469 The main change is due to changing the signature of  the ConvertOscillationScores2Events() method

Update Oscillations2012.cs

Issue #469
1: Delete the GetOscillationFrequency() method
2: Change the way a new Oscillation event is initialised.

Update GenericRecognizerTests.cs

Issue #469 1: Write a new test method. Its original purpose was to satisfy Anthony's intention of having two profiles with different Windows. This was a way to get the plot scaling fixed. Unfortunately a lot of the functionality to do with the OscillationEvent class was not working. I used this test method to get it working.

Update OscillationEvent.cs

Issue #469 Rejig the calculation of the oscillation period to make it more accurate.

Adjust start and end time test results

Issue #469 1: Adjust event expected start and end times for test results involving oscillations. These adjustments brought about by tightening the bounds of an oscillation event.
2: Add periodicity result into the test. The periodicity is the property unique to oscillation events.

Update GenericRecognizerTests.cs

Issue #469 Change name of test method to match the profiles actually used.

Update GenericRecognizerTests.cs

Issue #469 Update name of the test method a third time! At present there is no method to convert type AcousticEvent directly to type BlobEvent. Only to type SpectralEvent.

Update GenericRecognizerTests.cs

Issue #469 Change name of profile to be consistent with Blob profile name.

src/AnalysisPrograms/Recognizers/Base/MultiRecognizer.cs

@@ -64,15 +64,15 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
             MultiRecognizerConfig multiRecognizerConfig = (MultiRecognizerConfig)configuration;
 
             // make a standard spectrogram in which to render acoustic events and to append score tracks
-            // currently using Hamming window. Worth trying Hanning Window
             var config = new SonogramConfig
             {
+                WindowSize = 512,
+                WindowFunction = WindowFunctions.HANNING.ToString(),
                 NoiseReductionType = NoiseReductionType.Standard,
                 NoiseReductionParameter = 0.1,
-                WindowSize = 512,
             };
-            var sonogram = (BaseSonogram)new SpectrogramStandard(config, audioRecording.WavReader);
 
+            var spectrogram = (BaseSonogram)new SpectrogramStandard(config, audioRecording.WavReader);
             var scoreTracks = new List<Image<Rgb24>>();
             var plots = new List<Plot>();
             var events = new List<AcousticEvent>();
@@ -103,8 +103,8 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
 
                     newEvents.AddRange(output.NewEvents);
 
-                    // rescale scale of plots
-                    output.Plots.ForEach(p => p.ScaleDataArray(sonogram.FrameCount));
+                    // rescale all the plots to fit the current spectrogram.
+                    output.Plots.ForEach(p => p.ScaleDataArray(spectrogram.FrameCount));
 
                     plots.AddRange(output.Plots);
                 }
@@ -117,7 +117,7 @@ public override RecognizerResults Recognize(AudioRecording audioRecording, Confi
                 Events = events,
                 NewEvents = newEvents,
                 ScoreTrack = scoreTrackImage,
-                Sonogram = sonogram,
+                Sonogram = spectrogram,
                 Plots = plots,
                 Hits = null,
             };

src/AnalysisPrograms/Recognizers/Base/RecognizerBase.cs

@@ -380,7 +380,7 @@ protected virtual Image DrawSonogram(
             List<EventCommon> predictedEvents,
             double eventThreshold)
         {
-            var image = SpectrogramTools.GetSonogramPlusCharts(sonogram, predictedEvents, scores, hits);
+            var image = SpectrogramTools.GetSonogramPlusCharts(sonogram, predictedEvents, scores, hits, sonogram.Configuration.SourceFName);
             return image;
         }
 

src/AnalysisPrograms/Recognizers/Frogs/LitoriaFallax.cs

@@ -196,7 +196,7 @@ private void WriteDebugImage(
             bool displayDebugImage = MainEntry.InDEBUG;
             if (displayDebugImage)
             {
-                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits);
+                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits, sonogram.Configuration.SourceFName);
                 var debugPath1 =
                     outputDirectory.Combine(
                         FilenameHelpers.AnalysisResultName(
@@ -226,7 +226,7 @@ private void WriteDebugImage(
                             this.Identifier,
                             "png",
                             "DebugSpectrogram2"));
-                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null);
+                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null, sonogram.Configuration.SourceFName);
                 debugImage2.Save(debugPath2.FullName);
             }
         }

src/AnalysisPrograms/Recognizers/Frogs/LitoriaFreycineti.cs

@@ -190,7 +190,7 @@ private void WriteDebugImage(
             bool displayDebugImage = MainEntry.InDEBUG;
             if (displayDebugImage)
             {
-                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits);
+                Image debugImage1 = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, plots, hits, sonogram.Configuration.SourceFName);
                 var debugPath1 =
                     outputDirectory.Combine(
                         FilenameHelpers.AnalysisResultName(
@@ -220,7 +220,7 @@ private void WriteDebugImage(
                             this.Identifier,
                             "png",
                             "DebugSpectrogram2"));
-                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null);
+                Image debugImage2 = SpectrogramTools.GetSonogramPlusCharts(sonogram2, acousticEvents, plots, null, sonogram2.Configuration.SourceFName);
                 debugImage2.Save(debugPath2.FullName);
             }
         }

src/AnalysisPrograms/Recognizers/Frogs/LitoriaRothii.cs

@@ -222,7 +222,7 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
                 var lowPassPlot = new Plot("Low Pass", normalisedScores, normalisedThreshold);
 
                 var debugPlots = new List<Plot> { ampltdPlot, lowPassPlot, demeanedPlot, plot };
-                Image debugImage = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, debugPlots, null);
+                Image debugImage = SpectrogramTools.GetSonogramPlusCharts(sonogram, acousticEvents, debugPlots, null, sonogram.Configuration.SourceFName);
                 var debugPath = outputDirectory.Combine(FilenameHelpers.AnalysisResultName(Path.GetFileNameWithoutExtension(recording.BaseName), this.Identifier, "png", "DebugSpectrogram"));
                 debugImage.Save(debugPath.FullName);
             }

src/AnalysisPrograms/Recognizers/GenericRecognizer.cs

@@ -303,6 +303,13 @@ public static RecognizerResults RunProfiles(
                 }
             }
 
+            // Rescale the plots in case profiles used different window/frame lengths.
+            var lastSpectrogram = combinedResults.Sonogram;
+            combinedResults.Plots.ForEach(plot =>
+            {
+                plot.ScaleDataArray(lastSpectrogram.FrameCount);
+            });
+
             return combinedResults;
         }
 
@@ -425,10 +432,11 @@ public static RecognizerResults RunOneProfile(
             };
 
             //add info about decibel threshold into the event.
-            //This info is used later during post-processing of events.
+            //This info is used later during post-processing of events and for drawing of events.
             foreach (var ev in spectralEvents)
             {
                 ev.DecibelDetectionThreshold = decibelThreshold.Value;
+                ev.SegmentDurationSeconds = spectrogram.Duration.TotalSeconds;
             }
 
             allResults.NewEvents.AddRange(spectralEvents);
@@ -459,7 +467,7 @@ public override void SummariseResults(
         /// </summary>
         public static string SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
         {
-            var image3 = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.NewEvents, results.Plots, null);
+            var image3 = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.NewEvents, results.Plots, null, baseName);
 
             var path = Path.Combine(outputDirectory.FullName, baseName + ".profile.png");
             image3.Save(path);

src/AnalysisPrograms/Recognizers/PteropusSpecies.cs

@@ -464,8 +464,7 @@ internal static BaseSonogram GetSonogram(Config configuration, AudioRecording au
         /// </summary>
         internal static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
         {
-            //var image = sonogram.GetImageFullyAnnotated("Test");
-            var image = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.Events, results.Plots, null);
+            var image = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.Events, results.Plots, null, results.Sonogram.Configuration.SourceFName);
             image.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
         }
     }

src/AudioAnalysisTools/Events/Types/BlobEvent.cs

@@ -66,8 +66,6 @@ public static (List<EventCommon> Events, List<Plot> DecibelPlots) GetBlobEvents(
 
             var events = acEvents.ConvertAcousticEventsToSpectralEvents();
             spectralEvents.AddRange(events);
-            plots.Add(plot);
-
             return (spectralEvents, plots);
         }
 

src/AudioAnalysisTools/Events/Types/OscillationEvent.cs

@@ -5,9 +5,13 @@
 namespace AudioAnalysisTools
 {
     using System;
+    using System.Collections.Generic;
     using AudioAnalysisTools.Events;
     using AudioAnalysisTools.Events.Drawing;
+    using AudioAnalysisTools.StandardSpectrograms;
+    using SixLabors.ImageSharp;
     using SixLabors.ImageSharp.Processing;
+    using TowseyLibrary;
 
     public class OscillationEvent : SpectralEvent
     {
@@ -17,17 +21,82 @@ public OscillationEvent()
 
         // TODO: add extra metadata!!!
 
+        /// <summary>
+        /// Gets or sets the period in seconds between consecutive high points in an oscillation event.
+        /// </summary>
+        public double Periodicity { get; set; }
+
+        /// <summary>
+        /// Draws a border around this oscillation event.
+        /// </summary>
         public override void Draw(IImageProcessingContext graphics, EventRenderingOptions options)
         {
-            // foreach (var track in tracks) {
-            // track.Draw(...)
-            // }
+            if (options.DrawBorder)
+            {
+                var border = options.Converters.GetPixelRectangle(this);
+                graphics.NoAA().DrawBorderInset(options.Border, border);
+            }
+
+            this.DrawScoreIndicator(graphics, options);
+            this.DrawEventLabel(graphics, options);
+        }
+
+        /// <summary>
+        /// Extracts an event from a spectrogram given its bounds.
+        /// Then trims the event because oscillation events do not typically start where the DCT places them.
+        /// It a;sp returns the periodicity of the oscillation event.
+        /// </summary>
+        public static (int EventStart, int EventEnd, double FramePeriod) TrimEvent(SpectrogramStandard spectrogram, int startFrame, int minBin, int endFrame, int maxBin)
+        {
+            //obtain the oscillation event's periodicity.
+            //extract the relevant portion of the spectrogram.
+            var eventMatrix = MatrixTools.Submatrix<double>(spectrogram.Data, startFrame, minBin, endFrame, maxBin);
+            var frameAverages = MatrixTools.GetRowAverages(eventMatrix);
+            frameAverages = DataTools.normalise(frameAverages);
+            double threshold = 0.25;
+
+            // find the true start frame
+            int startFrameOffset = 0;
+            for (int frame = 1; frame < frameAverages.Length; frame++)
+            {
+                startFrameOffset++;
+                if (frameAverages[frame - 1] < threshold && frameAverages[frame] >= threshold)
+                {
+                    break;
+                }
+            }
+
+            int endFrameOffset = 0;
+            for (int frame = frameAverages.Length - 1; frame >= 0; frame--)
+            {
+                endFrameOffset++;
+                if (frameAverages[frame - 1] >= threshold && frameAverages[frame] < threshold)
+                {
+                    break;
+                }
+            }
+
+            int trueStartFrame = startFrame + startFrameOffset;
+            int trueEndFrame = endFrame - endFrameOffset;
+
+            // determine the number of times the frame values step from below to above threshold.
+            // also the frame index in which the steps happen.
+            int stepCount = 0;
+            var peakOnsets = new List<int>();
+            for (int frame = 1; frame < frameAverages.Length; frame++)
+            {
+                if (frameAverages[frame - 1] < threshold && frameAverages[frame] >= threshold)
+                {
+                    stepCount++;
+                    peakOnsets.Add(frame);
+                }
+            }
 
-            //this.Track.Draw(graphics, options);
+            // calculate the length of a whole number of complete periods.
+            int framePeriods = peakOnsets[peakOnsets.Count - 1] - peakOnsets[0];
+            double framePeriod = framePeriods / (double)(stepCount - 1);
 
-            //  base drawing (border)
-            // TODO: unless border is disabled
-            base.Draw(graphics, options);
+            return (trueStartFrame, trueEndFrame, framePeriod);
         }
     }
 }