Fix various bugs in the drawing of events on spectrograms.

Issue #297

src/AnalysisBase/AnalysisResult2.cs

@@ -56,6 +56,12 @@ public AnalysisResult2(AnalysisSettings settingsUsed, SegmentSettingsBase segmen
         /// </summary>
         public EventBase[] Events { get; set; }
 
+        /// <summary>
+        /// Gets or sets event results.
+        /// Should typically contain many results.
+        /// </summary>
+        public EventBase[] NewEvents { get; set; }
+
         /// <summary>
         /// Gets or sets summary indices results.
         /// Should typically contain just 1 result.

src/AnalysisBase/ResultBases/ResultBase.cs

@@ -18,8 +18,6 @@ namespace AnalysisBase.ResultBases
     /// </summary>
     public abstract class ResultBase : IComparable<ResultBase>, IComparable
     {
-        private double resultStartSeconds;
-
         /// <summary>
         /// Gets or sets the filename of the audio file this result produced.
         /// </summary>
@@ -35,19 +33,7 @@ public abstract class ResultBase : IComparable<ResultBase>, IComparable
         /// E.g. Given segment 78 of a 120min audio file, with a segment size of 60 seconds, this property would hold 78 minutes.
         /// And again: StartOffset is the time offset between the start of the recording and the start of the current result.
         /// </remarks>
-        public double ResultStartSeconds
-        {
-            get
-            {
-                return this.resultStartSeconds;
-            }
-
-            set
-            {
-                this.ResultMinute = (int)(value / 60.0);
-                this.resultStartSeconds = value;
-            }
-        }
+        public virtual double ResultStartSeconds { get; set; }
 
         /// <summary>
         /// Gets or sets the duration of audio segment that produced this result.
@@ -58,9 +44,9 @@ public double ResultStartSeconds
 
         /// <summary>
         /// Gets the ResultMinute.
-        /// This is an integer representation of <see cref="ResultStartSeconds"/>.
+        /// This is the floored integer minute of <see cref="ResultStartSeconds"/>.
         /// </summary>
-        public int ResultMinute { get; private set; }
+        public int ResultMinute => (int)(this.ResultStartSeconds / 60.0);
 
         /// <summary>
         /// Defines an innate order of Analysis results based on the <c>SegmentStartOffset</c>.

src/AnalysisPrograms/AnalyseLongRecordings/AnalyseLongRecording.cs

@@ -404,7 +404,15 @@ private static void Cleanup(Arguments args, FileInfo configFile)
         {
             if (args.WhenExitCopyConfig && args.Config.NotNull())
             {
-                configFile.CopyTo(Path.Combine(args.Output.FullName, Path.GetFileName(args.Config)), true);
+                var destination = Path.Combine(args.Output.FullName, Path.GetFileName(args.Config));
+                if (configFile.FullName == destination)
+                {
+                    Log.Warn("Cannot copy config file to output directory because source = destination.");
+                }
+                else
+                {
+                    configFile.CopyTo(Path.Combine(args.Output.FullName, Path.GetFileName(args.Config)), true);
+                }
             }
 
             if (args.WhenExitCopyLog && MainEntry.Logging.LogFileName.NotNull())

src/AnalysisPrograms/Recognizers/Base/RecognizerBase.cs

@@ -20,6 +20,8 @@ namespace AnalysisPrograms.Recognizers.Base
     using AnalysisBase;
     using AnalysisBase.ResultBases;
     using AudioAnalysisTools;
+    using AudioAnalysisTools.Events;
+    using AudioAnalysisTools.Events.Types;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.StandardSpectrograms;
     using AudioAnalysisTools.WavTools;
@@ -100,12 +102,13 @@ public override AnalysisResult2 Analyze<T>(AnalysisSettings analysisSettings, Se
 
             BaseSonogram sonogram = results.Sonogram;
             double[,] hits = results.Hits;
-            var predictedEvents = results.Events;
+            var predictedEvents = results.GetAllEvents();
 
             // double check all the events have the right offset in case it was missed
             foreach (var predictedEvent in predictedEvents)
             {
                 predictedEvent.SegmentStartSeconds = segmentSettings.SegmentStartOffset.TotalSeconds;
+                predictedEvent.SegmentDurationSeconds = recording.Duration.TotalSeconds;
             }
 
             analysisResults.Events = predictedEvents.ToArray();
@@ -147,7 +150,10 @@ public override AnalysisResult2 Analyze<T>(AnalysisSettings analysisSettings, Se
                 const double EventThreshold = 0.1;
                 var plots = results.Plots ?? new List<Plot>();
 
-                Image image = this.DrawSonogram(sonogram, hits, plots, predictedEvents, EventThreshold);
+                //TODO Remove this when we remove AcousticEvent.
+                var convertedEvents = predictedEvents.Select(ec => ec is AcousticEvent ae ? EventConverters.ConvertAcousticEventToSpectralEvent(ae) : (EventCommon)ec).ToList();
+
+                Image image = this.DrawSonogram(sonogram, hits, plots, convertedEvents, EventThreshold);
                 image.Save(imagePath);
                 analysisResults.ImageFile = segmentSettings.SegmentImageFile;
 
@@ -292,7 +298,9 @@ private void SummarizeHighResolutionIndices(
 
         public override void WriteEventsFile(FileInfo destination, IEnumerable<EventBase> results)
         {
-            Csv.WriteToCsv(destination, results.Select(x => (AcousticEvent)x));
+            // TODO check this
+            //Csv.WriteToCsv(destination, results.Select(x => (AcousticEvent)x));
+            Csv.WriteToCsv(destination, results.Select(x => (EventCommon)x));
         }
 
         public override void WriteSummaryIndicesFile(FileInfo destination, IEnumerable<SummaryIndexBase> results)
@@ -329,7 +337,7 @@ protected virtual Image DrawSonogram(
             BaseSonogram sonogram,
             double[,] hits,
             List<Plot> scores,
-            List<AcousticEvent> predictedEvents,
+            List<EventCommon> predictedEvents,
             double eventThreshold)
         {
             var image = SpectrogramTools.GetSonogramPlusCharts(sonogram, predictedEvents, scores, hits);

src/AudioAnalysisTools/Events/Types/CompositeEvent.cs

@@ -28,6 +28,8 @@ public CompositeEvent(List<SpectralEvent> events)
         public override double EventStartSeconds =>
             this.ComponentEvents.Min(x => x.EventStartSeconds);
 
+        public override double ResultStartSeconds => this.EventStartSeconds;
+
         public override double EventEndSeconds =>
             this.ComponentEvents.Max(x => (x as ITemporalEvent)?.EventEndSeconds) ?? double.PositiveInfinity;
 

src/AudioAnalysisTools/Tracks/ForwardTrackAlgorithm.cs

@@ -105,7 +105,8 @@ public static (List<EventCommon> Events, double[] CombinedIntensity) GetForwardT
             // This will help in some cases to combine related events.
             if (parameters.CombinePossibleSyllableSequence)
             {
-                returnEvents = CompositeEvent.CombineSimilarProximalEvents(events, parameters.SyllableStartDifference, parameters.SyllableHertzGap);
+                var timeDiff = TimeSpan.FromSeconds(parameters.SyllableStartDifference);
+                returnEvents = CompositeEvent.CombineSimilarProximalEvents(events, timeDiff, parameters.SyllableHertzGap);
             }
 
             return (returnEvents, combinedIntensityArray);
@@ -229,7 +230,7 @@ public static Track GetForwardTrack(double[,] peaks, int startRow, int startBin,
                 track.SetPoint(row, bin, maxValue);
 
                 // next line is for debug purposes
-                var info = track.CheckPoint(row, bin);
+                //var info = track.CheckPoint(row, bin);
             }
 
             return track;

src/AudioAnalysisTools/Tracks/ForwardTrackParameters.cs

@@ -33,7 +33,7 @@ public class ForwardTrackParameters : CommonParameters
         /// </summary>
         public bool CombinePossibleSyllableSequence { get; set; }
 
-        public TimeSpan SyllableStartDifference { get; set; }
+        public double SyllableStartDifference { get; set; }
 
         public int SyllableHertzGap { get; set; }
     }

tests/Acoustics.Test/AnalysisPrograms/Recognizers/GenericRecognizer/GenericRecognizerTests.cs

@@ -405,7 +405,7 @@ public void TestForwardTrackAlgorithm()
                 HarmonicsStartDifference = TimeSpan.FromSeconds(0.2),
                 HarmonicsHertzGap = 200,
                 CombinePossibleSyllableSequence = false,
-                SyllableStartDifference = TimeSpan.FromSeconds(0.2),
+                SyllableStartDifference = 0.2,
                 SyllableHertzGap = 300,
             };