Merge pull request #211 from QutEcoacoustics/Second-Fix-to-Issue-#199

Adds rendering of ALL grayscale LD spectrograms to standard indices generation. Closes #199 (again)

src/AnalysisConfigFiles/IndexPropertiesConfig.yml

@@ -613,7 +613,7 @@ DIF:
   Comment: "Spectrum of summed DIFFERENCES between consecutive FFT coeff's in the ampl spgram. This spgram not displayed. It is used as intermediate for subsequent calculation of ACI."
   DataType: double[]
   DefaultValue: 0.0
-  DoDisplay: true
+  DoDisplay: false
   NormMin: 0.0
   NormMax: 10.0
   CalculateNormMin: false
@@ -650,8 +650,8 @@ OSC:
   DataType: double[]
   DefaultValue: 0.0
   DoDisplay: true
-  NormMin: 0.0
-  NormMax: 10.0
+  NormMin: 0.1
+  NormMax: 5.0
   CalculateNormMin: true
   CalculateNormMax: true
   ProjectID: Acoustic Indices
@@ -661,7 +661,7 @@ SUM:
   Comment: "Spectrum of summed FFT coefficients derived from the ampl spgram. This spgram not displayed. It is used for intermediate calculations only."
   DataType: double[]
   DefaultValue: 0.0
-  DoDisplay: true
+  DoDisplay: false
   NormMin: 0.0
   NormMax: 10.0
   CalculateNormMin: false
@@ -687,7 +687,7 @@ RHZ:
   DefaultValue: 0.0
   DoDisplay: true
   NormMin: 0.1
-  NormMax: 1.5
+  NormMax: 1.0
   CalculateNormMin: false
   CalculateNormMax: false
   ProjectID: Acoustic Indices
@@ -700,8 +700,8 @@ RVT:
   DoDisplay: true
   NormMin: 0.1
   NormMax: 0.4
-  CalculateNormMin: false
-  CalculateNormMax: false
+  CalculateNormMin: true
+  CalculateNormMax: true
   ProjectID: Acoustic Indices
   Units: "tracks/s"
 RPS:
@@ -712,8 +712,8 @@ RPS:
   DoDisplay: true
   NormMin: 0.0
   NormMax: 0.4
-  CalculateNormMin: false
-  CalculateNormMax: false
+  CalculateNormMin: true
+  CalculateNormMax: true
   ProjectID: Acoustic Indices
   Units: "tracks/s"
 RNG:
@@ -724,8 +724,8 @@ RNG:
   DoDisplay: true
   NormMin: 0.0
   NormMax: 0.4
-  CalculateNormMin: false
-  CalculateNormMax: false
+  CalculateNormMin: true
+  CalculateNormMax: true
   ProjectID: Acoustic Indices
   Units: "tracks/s"
 R3D:
@@ -736,8 +736,8 @@ R3D:
   DoDisplay: true
   NormMin: 0.15
   NormMax: 1.0
-  CalculateNormMin: false
-  CalculateNormMax: false
+  CalculateNormMin: true
+  CalculateNormMax: true
   ProjectID: Acoustic Indices
   Units: "tracks/s"
 SPT:

src/AnalysisPrograms/Sandpit.cs

@@ -6,7 +6,6 @@ namespace AnalysisPrograms
 {
     using System;
     using System.Collections.Generic;
-    using System.Diagnostics;
     using System.Drawing;
     using System.Drawing.Imaging;
     using System.Globalization;
@@ -16,17 +15,15 @@ namespace AnalysisPrograms
     using System.Threading.Tasks;
     using Acoustics.Shared;
     using Acoustics.Shared.Csv;
-    using AnalyseLongRecordings;
+    using AnalysisPrograms.AnalyseLongRecordings;
     using AudioAnalysisTools;
     using AudioAnalysisTools.DSP;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.LongDurationSpectrograms;
     using AudioAnalysisTools.StandardSpectrograms;
     using AudioAnalysisTools.WavTools;
-    using log4net.Util;
     using McMaster.Extensions.CommandLineUtils;
-    using Production;
-    using Production.Arguments;
+    using AnalysisPrograms.Production.Arguments;
     using TowseyLibrary;
 
     /// <summary>
@@ -74,6 +71,7 @@ public override Task<int> Execute(CommandLineApplication app)
                 //CodeToPlaceScoreTracksUnderSingleImage();
 
                 //ConcatenateIndexFilesAndSpectrograms();
+                ConcatenateGreyScaleSpectrogramImages();
                 //ConcatenateMarineImages();
                 //ConcatenateImages();
                 //ConcatenateTwelveImages();
@@ -323,6 +321,10 @@ public static void Audio2CsvOverOneFile()
             //string outputPath = @"G:\SensorNetworks\Output\BradLaw\Pillaga24";
             //string configPath = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
+            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_001652.wav";
+            string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\01";
+            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
+
             // Ivan Campos recordings
             //string recordingPath = @"G:\SensorNetworks\WavFiles\Ivancampos\INCIPO01_20161031_024006_898.wav";
             //string outputPath = @"G:\SensorNetworks\Output\IvanCampos\17";
@@ -384,11 +386,11 @@ public static void Audio2CsvOverOneFile()
             //string outputPath = @"C:\Ecoacoustics\Output\SERF\SERFIndicesNew_2013June19";
             //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
-            // USE 24-hour data or parts of from MEZ, TASMAn ISLAND, liz Znidersic
+          // USE 24-hour data or parts of from MEZ, TASMAn ISLAND, liz Znidersic
             // these are six hour recordings
-            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_031652.wav";
-            string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\04";
-            string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
+            //string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_031652.wav";
+            //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\04";
+            //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
             // GROUND PARROT
             //string recordingPath = @"C:\SensorNetworks\WavFiles\TestRecordings\groundParrot_Perigian_TEST.wav";
@@ -1056,11 +1058,60 @@ public static void ConcatenateIndexFilesAndSpectrograms()
         }
 
         /// <summary>
-        /// read a set of Spectral index files and extract values from frequency band
-        /// This work done for Liz Znidersic paper.
-        /// End of the method requires access to Liz tagging info.
+        /// TODO Combine the grey scale spectrograms produced by AnalysisPrograms.exe
+        /// This method will be useful for comparing the response of different spectral indices to the same acoustic event.
+        /// Use this when you want best acoustic features for doing ML using spectral index features.
         /// </summary>
-        public static void ExtractSpectralFeatures()
+        public static void ConcatenateGreyScaleSpectrogramImages()
+        {
+
+            var ipDirInfo = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\01\Towsey.Acoustic");
+            var opDirInfo = new DirectoryInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\01\Towsey.Acoustic");
+            var opFileName = "SM304256_0+1_20151114_001652";
+
+            //string[] keys = { "ACI", "BGN", "CVR", "ENT", "EVN", "OSC", "PMN", "R3D", "RHZ", "RNG", "RPS", "RVT", "SPT" };
+            var keys = SpectralIndexValues.Keys;
+
+            //Read list of images into List
+            var listOfImages = new List<Image>();
+
+            foreach (var key in keys)
+            {
+                if (key == "DIF" || key == "SUM")
+                {
+                    continue;
+                }
+
+                // construct the path
+                //var path = Path.Combine(ipDirInfo.FullName, opFileName + key + ".png");
+                var path = FilenameHelpers.AnalysisResultPath(ipDirInfo, opFileName, key, "png");
+                var indexImage = ImageTools.ReadImage2Bitmap(path);
+
+                listOfImages.Add(indexImage);
+            }
+
+            var opPath = FilenameHelpers.AnalysisResultPath(opDirInfo, opFileName, "KEYS", "png");
+
+            // check how wide combined image will be. If tracks are wider than 180 = 3 hours, then go vertical
+            int imageCount = listOfImages.Count;
+            if (listOfImages[0].Width * imageCount > 180 * imageCount)
+            {
+                var combinedImage = ImageTools.CombineImagesVertically(listOfImages);
+                combinedImage?.Save(opPath);
+            }
+            else
+            {
+                var combinedImage = ImageTools.CombineImagesInLine(listOfImages);
+                combinedImage?.Save(opPath);
+            }
+        }
+
+    /// <summary>
+    /// read a set of Spectral index files and extract values from frequency band
+    /// This work done for Liz Znidersic paper.
+    /// End of the method requires access to Liz tagging info.
+    /// </summary>
+    public static void ExtractSpectralFeatures()
         {
             // parameters
             string dir =

src/AudioAnalysisTools/DSP/FrequencyScale.cs

@@ -1,4 +1,4 @@
-// <copyright file="FrequencyScale.cs" company="QutEcoacoustics">
+// <copyright file="FrequencyScale.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>
 
@@ -396,9 +396,11 @@ public static void DrawFrequencyLinesOnImage(Bitmap bmp, int[,] gridLineLocation
             for (int b = 0; b < bandCount; b++)
             {
                 int y = height - gridLineLocations[b, 0];
+                int hertzValue = gridLineLocations[b, 1];
+
                 if (y > 1)
                 {
-                    g.DrawString($"{gridLineLocations[b, 1]}", new Font("Thachoma", 8), txtColour, 1, y);
+                    g.DrawString($"{hertzValue}", new Font("Thachoma", 8), txtColour, 1, y);
                 }
             }
         } //end AddHzGridLines()

src/AudioAnalysisTools/LongDurationSpectrograms/LDSpectrogramRGB.cs

@@ -36,6 +36,7 @@ namespace AudioAnalysisTools.LongDurationSpectrograms
     using System.Collections.Generic;
     using System.Diagnostics;
     using System.Drawing;
+    using System.Drawing.Drawing2D;
     using System.Drawing.Imaging;
     using System.Globalization;
     using System.IO;
@@ -476,6 +477,12 @@ public void LoadSpectrogramDictionary(Dictionary<string, double[,]> dictionary)
                     {
                         minBound = indexProperties.NormMin;
                     }
+
+                    // Do not want OSC min set too low. Happens because min can = zero
+                    if (key.Equals("OSC") && minBound < indexProperties.NormMin)
+                    {
+                        minBound = indexProperties.NormMin;
+                    }
                 }
 
                 if (indexProperties.CalculateNormMax)
@@ -488,6 +495,15 @@ public void LoadSpectrogramDictionary(Dictionary<string, double[,]> dictionary)
                         maxBound = this.IndexStats[key].Maximum * 0.1;
                     }
                 }
+
+                // In some rare cases the resulting range is zero which will produce NaNs when normalized.
+                // In this case we just reset the bounds backs to the defaults in the config file.
+                // ReSharper disable once CompareOfFloatsByEqualityOperator - we are interested in ranges that are exactly zero distance
+                if (maxBound == minBound)
+                {
+                    minBound = indexProperties.NormMin;
+                    maxBound = indexProperties.NormMax;
+                }
             }
 
             // check min, max values
@@ -499,16 +515,6 @@ public void LoadSpectrogramDictionary(Dictionary<string, double[,]> dictionary)
             return matrix;
         }
 
-        /// <summary>
-        /// Draws all available spectrograms in grey scale
-        /// </summary>
-        public void DrawGreyScaleSpectrograms(DirectoryInfo opdir, string opFileName)
-        {
-            var keys = SpectralIndexValues.Keys;
-            //string[] keys = this.SpectrogramKeys;
-            this.DrawGreyScaleSpectrograms(opdir, opFileName, keys);
-        }
-
         /// <summary>
         /// draws only those spectrograms in the passed array of keys
         /// </summary>
@@ -540,16 +546,31 @@ public void DrawGreyScaleSpectrograms(DirectoryInfo opdir, string opFileName, st
                     continue;
                 }
 
-                // the directory for the following path must exist
-                var path = FilenameHelpers.AnalysisResultPath(opdir, opFileName, key, "png");
+                var ipList = this.GetSpectralIndexProperties();
+                if (!ipList[key].DoDisplay)
+                {
+                    continue;
+                }
+
                 var bmp = this.DrawGreyscaleSpectrogramOfIndex(key);
-                bmp?.Save(path);
+
+                var header = new Bitmap(bmp.Width, 20);
+                Graphics g = Graphics.FromImage(header);
+                g.Clear(Color.LightGray);
+                g.SmoothingMode = SmoothingMode.AntiAlias;
+                //g.InterpolationMode = InterpolationMode.HighQualityBicubic;
+                //g.PixelOffsetMode = PixelOffsetMode.HighQuality;
+                g.DrawString(key, new Font("Tahoma", 9), Brushes.Black, 4, 4);
+                var indexImage = ImageTools.CombineImagesVertically(new List<Image>(new Image[] { header, bmp }));
+
+                // save the image - the directory for the path must exist
+                var path = FilenameHelpers.AnalysisResultPath(opdir, opFileName, key, "png");
+                indexImage?.Save(path);
             }
         }
 
         /// <summary>
-        /// Assume calling method has done all the reality checks
-        /// </summary>
+        /// Assume calling method has done all the reality checks </summary>
         public Image DrawGreyscaleSpectrogramOfIndex(string key)
         {
             var matrix = this.GetNormalisedSpectrogramMatrix(key);
@@ -1475,11 +1496,19 @@ public static Tuple<Image, string>[] DrawSpectrogramsFromSpectralIndices(
             cs1.IndexStats = indexStatistics;
 
             // draw gray scale spectrogram for each index.
-            string[] keys = colorMap1.Split('-');
-            cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);
-            keys = colorMap2.Split('-');
+            //string[] keys = colorMap1.Split('-');
+            //cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);
+            //keys = colorMap2.Split('-');
+            // draw all available gray scale index spectrograms.
+            var keys = SpectralIndexValues.Keys;
             cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);
 
+            //    //string[] keys = this.SpectrogramKeys;
+            //cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);
+            //}
+            //keys = colorMap2.Split('-');
+            //cs1.DrawGreyScaleSpectrograms(outputDirectory, fileStem, keys);
+
             // create and save first false-colour spectrogram image
             var image1NoChrome = cs1.DrawFalseColourSpectrogramChromeless(cs1.ColorMode, colorMap1);
             Image image1 = null;

tests/Acoustics.Test/AnalysisPrograms/AnalyzeLongRecordings/TestAnalyzeLongRecording.cs

@@ -98,7 +98,7 @@ public void TestAnalyzeSr22050Recording()
             var resultsDirectory = this.outputDirectory.Combine("Towsey.Acoustic");
             var listOfFiles = resultsDirectory.EnumerateFiles().ToArray();
 
-            Assert.AreEqual(31, listOfFiles.Length);
+            Assert.AreEqual(38, listOfFiles.Length);
 
             var csvCount = listOfFiles.Count(f => f.Name.EndsWith(".csv"));
             Assert.AreEqual(16, csvCount);
@@ -107,7 +107,7 @@ public void TestAnalyzeSr22050Recording()
             Assert.AreEqual(2, jsonCount);
 
             var pngCount = listOfFiles.Count(f => f.Name.EndsWith(".png"));
-            Assert.AreEqual(13, pngCount);
+            Assert.AreEqual(20, pngCount);
 
             var twoMapsImagePath = resultsDirectory.CombineFile("TemporaryRecording1__2Maps.png");
             var twoMapsImage = ImageTools.ReadImage2Bitmap(twoMapsImagePath.FullName);
@@ -266,10 +266,10 @@ public void TestAnalyzeSr64000Recording()
                     analysisType: analysisType,
                     indexSpectrograms: dictionaryOfSpectra);
 
-            // test number of images - should now be 14
+            // test number of images - should now be 23
             listOfFiles = resultsDirectory.EnumerateFiles().ToArray();
             pngCount = listOfFiles.Count(f => f.Name.EndsWith(".png"));
-            Assert.AreEqual(14, pngCount);
+            Assert.AreEqual(21, pngCount);
 
             var twoMapsImagePath = resultsDirectory.CombineFile(recordingName + "__2Maps.png");
             var twoMapsImage = ImageTools.ReadImage2Bitmap(twoMapsImagePath.FullName);