Issue300 fix debug spectrograms

src/AnalysisBase/ResultBases/EventBase.cs

@@ -1,4 +1,4 @@
-// --------------------------------------------------------------------------------------------------------------------
+// --------------------------------------------------------------------------------------------------------------------
 // <copyright file="EventBase.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>
@@ -12,14 +12,14 @@ namespace AnalysisBase.ResultBases
     using System;
 
     /// <summary>
-    /// The base class for all Event style results
+    /// The base class for all Event style results.
     /// </summary>
     public abstract class EventBase : ResultBase
     {
         private double eventStartSeconds;
 
         /// <summary>
-        /// Gets or sets the time the current audio segment is offset from the start of the file/recording.
+        /// Gets or sets the time (in seconds) from start of the file/recording to start of the current audio segment.
         /// </summary>
         /// <remarks>
         /// <see cref="EventStartSeconds"/> will always be greater than or equal to <see cref="SegmentStartSeconds"/>.
@@ -36,7 +36,7 @@ public abstract class EventBase : ResultBase
         /// </summary>
         /// <remarks>
         /// 2017-09: This field USED to be offset relative to the current segment.
-        /// 2017-09: This field is NOW equivalent to <see cref="ResultBase.ResultStartSeconds"/>
+        /// 2017-09: This field is NOW equivalent to <see cref="ResultBase.ResultStartSeconds"/>.
         /// </remarks>
         public virtual double EventStartSeconds
         {
@@ -60,6 +60,13 @@ public virtual double EventStartSeconds
         /// </summary>
         public virtual double? LowFrequencyHertz { get; protected set; }
 
+        /// <summary>
+        /// Sets both the Segment start and the Event start.
+        /// <paramref name="segmentStart"/> is measured relative to the start of the recording.
+        /// <paramref name="eventStartSegmentRelative"/> is measured relative to the start of the segment.
+        /// This method sets both <see cref="SegmentStartSeconds"/> and <see cref="EventStartSeconds"/> which
+        /// are both measured relative to the start of the recording.
+        /// </summary>
         protected void SetEventStartRelative(TimeSpan segmentStart, double eventStartSegmentRelative)
         {
             this.SegmentStartSeconds = segmentStart.TotalSeconds;

src/AnalysisPrograms/AnalyseLongRecordings/AnalyseLongRecording.cs

@@ -73,7 +73,8 @@ public static void Execute(Arguments arguments)
             {
                 Log.Warn($"Config file {configFile.FullName} not found... attempting to resolve config file");
 
-                // we use .ToString() here to get the original input string - Using fullname always produces an absolute path wrt to pwd... we don't want to prematurely make asusmptions:
+                // we use .ToString() here to get the original input string.
+                // Using fullname always produces an absolute path relative to pwd... we don't want to prematurely make assumptions:
                 // e.g. We require a missing absolute path to fail... that wouldn't work with .Name
                 // e.g. We require a relative path to try and resolve, using .FullName would fail the first absolute check inside ResolveConfigFile
                 configFile = ConfigFile.Resolve(configFile.ToString(), Directory.GetCurrentDirectory().ToDirectoryInfo());

src/AnalysisPrograms/EventStatistics/EventStatisticsEntry.cs

@@ -49,7 +49,7 @@ public static async Task<int> ExecuteAsync(Arguments arguments)
                 Log.Warn($"Config file {config.FullName} not found... attempting to resolve config file");
 
                 // we use  the original input string - Using FileInfo fullname always produces an
-                // absolute path wrt to pwd... we don't want to prematurely make assumptions:
+                // absolute path relative to pwd... we don't want to prematurely make assumptions:
                 // e.g. We require a missing absolute path to fail... that wouldn't work with .Name
                 // e.g. We require a relative path to try and resolve, using .FullName would fail the first absolute
                 //    check inside ResolveConfigFile

src/AnalysisPrograms/OscillationRecogniser.cs

@@ -12,6 +12,7 @@ namespace AnalysisPrograms
     using System.Linq;
     using System.Text;
     using System.Threading.Tasks;
+    using Acoustics.Shared.Csv;
     using AudioAnalysisTools;
     using AudioAnalysisTools.StandardSpectrograms;
     using AudioAnalysisTools.WavTools;
@@ -126,15 +127,10 @@ public static void Execute(Arguments arguments)
                 pcHIF = 100 * hifCount / sonogram.FrameCount;
             }
 
-            //write event count to results file.
-            double sigDuration = sonogram.Duration.TotalSeconds;
+            // write event count to results file.
             string fname = recordingFile.BaseName();
-            int count = predictedEvents.Count;
 
-            //string str = String.Format("#RecordingName\tDuration(sec)\t#Ev\tCompT(ms)\t%hiFrames\n{0}\t{1}\t{2}\t{3}\t{4}\n", fname, sigDuration, count, analysisDuration.TotalMilliseconds, pcHIF);
-            string str = string.Format("{0}\t{1}\t{2}\t{3}\t{4}", fname, sigDuration, count, analysisDuration.TotalMilliseconds, pcHIF);
-            StringBuilder sb = AcousticEvent.WriteEvents(predictedEvents, str);
-            FileTools.WriteTextFile(opPath, sb.ToString());
+            Csv.WriteToCsv(opPath.ToFileInfo(), predictedEvents);
 
             //draw images of sonograms
             string imagePath = outputDir + fname + ".png";

src/AnalysisPrograms/Recognizers/Base/RecognizerBase.cs

@@ -336,35 +336,6 @@ protected virtual Image DrawSonogram(
             double eventThreshold)
         {
             var image = SpectrogramTools.GetSonogramPlusCharts(sonogram, predictedEvents, scores, hits);
-
-            //const bool doHighlightSubband = false;
-            //const bool add1KHzLines = true;
-            //var image = new Image_MultiTrack(sonogram.GetImage(doHighlightSubband, add1KHzLines, doMelScale: false));
-            //image.AddTrack(ImageTrack.GetTimeTrack(sonogram.Duration, sonogram.FramesPerSecond));
-            //image.AddTrack(ImageTrack.GetSegmentationTrack(sonogram));
-
-            //if (scores != null)
-            //{
-            //    foreach (var plot in scores)
-            //    {
-            //        image.AddTrack(ImageTrack.GetNamedScoreTrack(plot.data, 0.0, 1.0, plot.threshold, plot.title));
-            //    }
-            //}
-
-            //if (hits != null)
-            //{
-            //    image.OverlayRedTransparency(hits);
-            //}
-
-            //if (predictedEvents != null && predictedEvents.Count > 0)
-            //{
-            //    image.AddEvents(
-            //        predictedEvents,
-            //        sonogram.NyquistFrequency,
-            //        sonogram.Configuration.FreqBinCount,
-            //        sonogram.FramesPerSecond);
-            //}
-
             return image;
         }
 

src/AnalysisPrograms/Recognizers/Base/WhistleParameters.cs

@@ -39,10 +39,6 @@ public static (List<AcousticEvent>, double[]) GetWhistles(
             double binWidth = nyquist / (double)binCount;
             int minBin = (int)Math.Round(minHz / binWidth);
             int maxBin = (int)Math.Round(maxHz / binWidth);
-            //int binCountInBand = maxBin - minBin + 1;
-
-            // buffer zone around whistle is four bins wide.
-            int N = 4;
 
             // list of accumulated acoustic events
             var events = new List<AcousticEvent>();
@@ -54,7 +50,8 @@ public static (List<AcousticEvent>, double[]) GetWhistles(
                 // set up an intensity array for the frequency bin.
                 double[] intensity = new double[frameCount];
 
-                if (minBin < N)
+                // buffer zone around whistle is four bins wide.
+                if (minBin < 4)
                 {
                     // for all time frames in this frequency bin
                     for (int t = 0; t < frameCount; t++)
@@ -110,33 +107,9 @@ public static (List<AcousticEvent>, double[]) GetWhistles(
             } //end for all freq bins
 
             // combine adjacent acoustic events
-            events = AcousticEvent.CombineOverlappingEvents(events);
+            events = AcousticEvent.CombineOverlappingEvents(events, segmentStartOffset);
 
             return (events, combinedIntensityArray);
         }
-
-        /*
-        /// <summary>
-        /// Calculates the average intensity in a freq band having min and max freq,
-        /// AND then subtracts average intensity in the side/buffer bands, below and above.
-        /// THis method adds dB log values incorrectly but it is faster than doing many log conversions.
-        /// This method is used to find acoustic events and is accurate enough for the purpose.
-        /// </summary>
-        public static double[] CalculateFreqBandAvIntensityMinusBufferIntensity(double[,] sonogramData, int minHz, int maxHz, int nyquist)
-        {
-            var bandIntensity = SNR.CalculateFreqBandAvIntensity(sonogramData, minHz, maxHz, nyquist);
-            var bottomSideBandIntensity = SNR.CalculateFreqBandAvIntensity(sonogramData, minHz - bottomHzBuffer, minHz, nyquist);
-            var topSideBandIntensity = SNR.CalculateFreqBandAvIntensity(sonogramData, maxHz, maxHz + topHzBuffer, nyquist);
-
-            int frameCount = sonogramData.GetLength(0);
-            double[] netIntensity = new double[frameCount];
-            for (int i = 0; i < frameCount; i++)
-            {
-                netIntensity[i] = bandIntensity[i] - bottomSideBandIntensity[i] - topSideBandIntensity[i];
-            }
-
-            return netIntensity;
-        }
-        */
     }
 }

src/AnalysisPrograms/Recognizers/GenericRecognizer.cs

@@ -325,18 +325,9 @@ private static Plot PreparePlot(double[] array, string title, double threshold)
         /// </summary>
         static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig, DirectoryInfo outputDirectory, string baseName)
         {
-            //var image1 = results.Sonogram.GetImage(false, true, false);
-            //image1.Save(Path.Combine("C:\\temp\\test1.profile.png"));
-
-            //var image2 = results.Sonogram.GetImageFullyAnnotated("Test");
-            //image2.Save(Path.Combine("C:\\temp\\test2.profile.png"));
-
             var image3 = SpectrogramTools.GetSonogramPlusCharts(results.Sonogram, results.Events, results.Plots, null);
 
-            //image3.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
-            image3.Save(Path.Combine("C:\\temp", baseName + ".profile.png"));
-
-            //sonogram.GetImageFullyAnnotated("test").Save("C:\\temp\\test.png");
+            image3.Save(Path.Combine(outputDirectory.FullName, baseName + ".profile.png"));
         }
 
         /// <inheritdoc cref="RecognizerConfig"/> />

src/AnalysisPrograms/Recognizers/LewiniaPectoralis.cs

@@ -1,4 +1,4 @@
-// --------------------------------------------------------------------------------------------------------------------
+// --------------------------------------------------------------------------------------------------------------------
 // <copyright file="LewiniaPectoralis.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>
@@ -193,14 +193,6 @@ public override RecognizerResults Recognize(
                     prunedEvents.Add(ae);
                 }
 
-                // do a recognizer TEST.
-                if (false)
-                {
-                    var testDir = new DirectoryInfo(outputDirectory.Parent.Parent.FullName);
-                    TestTools.RecognizerScoresTest(recording.BaseName, testDir, recognizerConfig.AnalysisName, scoreArray);
-                    AcousticEvent.TestToCompareEvents(recording.BaseName, testDir, recognizerConfig.AnalysisName, predictedEvents);
-                }
-
                 // increase very low scores
                 for (int j = 0; j < scoreArray.Length; j++)
                 {

src/AnalysisPrograms/Recognizers/LitoriaBicolor.cs

@@ -152,14 +152,6 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
                 ae.SegmentDurationSeconds = recordingDuration.TotalSeconds;
             }
 
-            // do a RECOGNIZER TEST.
-            if (false)
-            {
-                var testDir = new DirectoryInfo(outputDirectory.Parent.Parent.FullName);
-                TestTools.RecognizerScoresTest(recording.BaseName, testDir, recognizerConfig.AnalysisName, scoreArray);
-                AcousticEvent.TestToCompareEvents(recording.BaseName, testDir, recognizerConfig.AnalysisName, predictedEvents);
-            }
-
             var plot = new Plot(this.DisplayName, scoreArray, recognizerConfig.EventThreshold);
             return new RecognizerResults()
             {
@@ -171,7 +163,7 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
         }
 
         /// <summary>
-        /// ################ THE KEY ANALYSIS METHOD
+        /// THE KEY ANALYSIS METHOD.
         /// </summary>
         /// <param name="recording"></param>
         /// <param name="sonoConfig"></param>

src/AnalysisPrograms/Recognizers/LitoriaWatjulumensis.cs

@@ -157,14 +157,6 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
                 ae.SegmentStartSeconds = segmentStartOffset.TotalSeconds;
             }
 
-            // do a recognizer TEST.
-            if (false)
-            {
-                var testDir = new DirectoryInfo(outputDirectory.Parent.Parent.FullName);
-                TestTools.RecognizerScoresTest(recording.BaseName, testDir, recognizerConfig.AnalysisName, scoreArray);
-                AcousticEvent.TestToCompareEvents(recording.BaseName, testDir, recognizerConfig.AnalysisName, predictedEvents);
-            }
-
             var plot = new Plot(this.DisplayName, scoreArray, recognizerConfig.EventThreshold);
             return new RecognizerResults()
             {
@@ -175,8 +167,8 @@ public override RecognizerResults Recognize(AudioRecording recording, Config con
             };
         }
 
-        ///  <summary>
-        ///  ################ THE KEY ANALYSIS METHOD for TRILLS
+        /// <summary>
+        /// ################ THE KEY ANALYSIS METHOD for TRILLS
         ///
         ///  See Anthony's ExempliGratia.Recognize() method in order to see how to use methods for config profiles.
         ///  </summary>