Fixing bugs in merging of acoustic events

Issue #300 The main difficulty here is confusing terminology of temporal  fileds and properties. Changed some of these to be more explicit.
There appears to remain one more bug - the number of acoustic events in the ae.csv file does not match number that appears in the spectrogram images??

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
         {
@@ -60,10 +60,13 @@ public virtual double EventStartSeconds
         /// </summary>
         public virtual double? LowFrequencyHertz { get; protected set; }
 
-        protected void SetEventStartRelative(TimeSpan segmentStart, double eventStartSegmentRelative)
+        /// <summary>
+        /// Sets both the Segment start and the Event start wrt to recording.
+        /// </summary>
+        protected void SetSegmentAndEventStartsWrtRecording(TimeSpan segmentStartWrtRecording, double eventStartWrtSegment)
         {
-            this.SegmentStartSeconds = segmentStart.TotalSeconds;
-            this.EventStartSeconds = this.SegmentStartSeconds + eventStartSegmentRelative;
+            this.SegmentStartSeconds = segmentStartWrtRecording.TotalSeconds;
+            this.EventStartSeconds = this.SegmentStartSeconds + eventStartWrtSegment;
         }
     }
 }

src/AnalysisPrograms/Recognizers/Base/WhistleParameters.cs

@@ -30,7 +30,7 @@ public static (List<AcousticEvent>, double[]) GetWhistles(
             double decibelThreshold,
             double minDuration,
             double maxDuration,
-            TimeSpan segmentStartOffset)
+            TimeSpan segmentStartWrtRecording)
         {
             var sonogramData = sonogram.Data;
             int frameCount = sonogramData.GetLength(0);
@@ -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++)
@@ -96,7 +93,7 @@ public static (List<AcousticEvent>, double[]) GetWhistles(
                     decibelThreshold,
                     minDuration,
                     maxDuration,
-                    segmentStartOffset);
+                    segmentStartWrtRecording);
 
                 // add to conbined intensity array
                 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, segmentStartWrtRecording);
 
             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

@@ -334,7 +334,7 @@ static void SaveDebugSpectrogram(RecognizerResults results, Config genericConfig
             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"));
+            //image3.Save(Path.Combine("C:\\temp", baseName + ".profile.png"));
 
             //sonogram.GetImageFullyAnnotated("test").Save("C:\\temp\\test.png");
         }