Finally get content description working in IAnalyzer2 environment.

Issue #252 Finally get content description working in IAnalyzer2 environment.

src/AnalysisPrograms/ContentDescription.cs

@@ -10,13 +10,11 @@ namespace AnalysisPrograms
     using System.IO;
     using System.Linq;
     using System.Reflection;
-    using Accord;
     using Acoustics.Shared;
     using Acoustics.Shared.ConfigFile;
     using Acoustics.Shared.Csv;
     using AnalysisBase;
     using AnalysisBase.ResultBases;
-    using AudioAnalysisTools;
     using AudioAnalysisTools.ContentDescriptionTools;
     using AudioAnalysisTools.Indices;
     using AudioAnalysisTools.LongDurationSpectrograms;
@@ -201,13 +199,18 @@ public override void SummariseResults(
 
             // now get the content description for each minute.
             //TODO TODO TODO TODO GET FILE NAME FROM CONFIG.YML FILE
-            var path1 = Path.Combine(configDirectory, ContentSignatures.TemplatesFileName);
-            var templatesFile = new FileInfo(path1);
-            var contentPlots = GetContentDescription(spectralIndices, templatesFile, startTimeOffset);
+            var templatesFile = new FileInfo(Path.Combine(configDirectory, ContentSignatures.TemplatesFileName));
+            var contentDictionary = GetContentDescription(spectralIndices, templatesFile, startTimeOffset);
+
+            // Write the results to a csv file
+            var filePath = Path.Combine(resultsDirectory.FullName, "AcousticSignatures.csv");
+            FileTools.WriteDictionaryAsCsvFile(contentDictionary, filePath);
+
+            // prepare graphical plots of the acoustic signatures.
+            var contentPlots = GetPlots(contentDictionary);
             var images = GraphsAndCharts.DrawPlotDistributions(contentPlots);
             var plotsImage = ImageTools.CombineImagesVertically(images);
-            var path2 = Path.Combine(resultsDirectory.FullName, "DistributionsOfContentScores.png");
-            plotsImage.Save(path2);
+            plotsImage.Save(Path.Combine(resultsDirectory.FullName, "DistributionsOfContentScores.png"));
 
             // Attach content description plots to LDFC spectrogram and write to file
             var ldfcSpectrogram = Image.FromFile(ldfcSpectrogramPath);
@@ -222,7 +225,10 @@ public override void SummariseResults(
         /// <param name="spectralIndices">set of spectral indices for each minute.</param>
         /// <param name="templatesFile">json file containing description of templates.</param>
         /// <param name="elapsedTimeAtStartOfRecording">minute Id for start of recording.</param>
-        public static List<Plot> GetContentDescription(SpectralIndexBase[] spectralIndices, FileInfo templatesFile, TimeSpan elapsedTimeAtStartOfRecording)
+        public static Dictionary<string, double[]> GetContentDescription(
+            SpectralIndexBase[] spectralIndices,
+            FileInfo templatesFile,
+            TimeSpan elapsedTimeAtStartOfRecording)
         {
             // Read in the content description templates
             var templates = Json.Deserialize<TemplateManifest[]>(templatesFile);
@@ -242,6 +248,15 @@ public static List<Plot> GetContentDescription(SpectralIndexBase[] spectralIndic
                 // Transfer acoustic indices to dictionary
                 var indicesDictionary = IndexCalculateSixOnly.ConvertIndicesToDictionary(oneMinuteOfIndices);
 
+                // normalize the index values
+                foreach (string key in ContentSignatures.IndexNames)
+                {
+                    var indexBounds = ContentSignatures.IndexValueBounds[key];
+                    var indexArray = indicesDictionary[key];
+                    var normalisedVector = DataTools.NormaliseInZeroOne(indexArray, indexBounds[0], indexBounds[1]);
+                    indicesDictionary[key] = normalisedVector;
+                }
+
                 // scan templates over one minute of indices
                 var resultsForOneMinute = ContentSignatures.AnalyzeOneMinute(
                     templates,
@@ -251,14 +266,21 @@ public static List<Plot> GetContentDescription(SpectralIndexBase[] spectralIndic
                 results.Add(resultsForOneMinute);
             }
 
-            // Write the results to file
-            // TODO TODO
-            var dictionaryOfScores = DataProcessing.ConvertResultsToArrays(results, length, startMinuteId);
-            var fileName = "zzz";
-            //DataProcessing.WriteScoresToFile(fileName);
-
+            // convert results to dictionary of score arrays
             // TODO TODO fix the below plotLength and start.
-            var plotDict = DataProcessing.ConvertResultsToPlots(results, 1440, 0);
+            var dictionaryOfScores = DataProcessing.ConvertResultsToDictionaryOfArrays(results, length, startMinuteId);
+            return dictionaryOfScores;
+        }
+
+        /// <summary>
+        /// Produce plots for graphical display.
+        /// NOTE: The threshold can be changed later.
+        /// </summary>
+        /// <returns>A list of graphical plots.</returns>
+        private static List<Plot> GetPlots(Dictionary<string, double[]> contentDictionary)
+        {
+            double threshold = 0.25;
+            var plotDict = DataProcessing.ConvertArraysToPlots(contentDictionary, threshold);
             var contentPlots = DataProcessing.ConvertPlotDictionaryToPlotList(plotDict);
 
             // convert scores to z-scores

src/AnalysisPrograms/Sandpit.cs

@@ -368,10 +368,10 @@ public static void Audio2CsvOverOneFile()
             //string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.Acoustic.yml";
 
             // Test on Content Description
-            string recordingPath = @"C:\Ecoacoustics\WavFiles\FlyingFox\20190115_Bellingen_Feeding.wav";
-            //string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652+1000.wav";
+            //string recordingPath = @"C:\Ecoacoustics\WavFiles\FlyingFox\20190115_Bellingen_Feeding.wav";
+            string recordingPath = @"C:\Ecoacoustics\WavFiles\LizZnidersic\TasmanIsland2015_Unit2_Mez\SM304256_0+1_20151114_131652+1000.wav";
             //string outputPath = @"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMez\14";
-            string outputPath = @"C:\Ecoacoustics\ContentDescription\TestOfSixIndices";
+            string outputPath = @"C:\Ecoacoustics\ContentDescription\Test6IndicesMez13";
             string configPath = @"C:\Work\GitHub\audio-analysis\src\AnalysisConfigFiles\Towsey.ContentDescription.yml";
 
             // Ivan Campos recordings

src/AudioAnalysisTools/ContentDescriptionTools/ContentSignatures.cs

@@ -21,7 +21,7 @@ public class ContentSignatures
 
         public const string AnalysisString = "__Towsey.Acoustic.";
 
-        //TODO TODO TODO TODO GET FILE NAME FROM CONFIG.YML FILE
+        //TODO TODO  GET FILE NAME FROM CONFIG.YML FILE
         public const string TemplatesFileName = "Towsey.TemplateDefinitions.json";
 
         /// <summary>
@@ -50,8 +50,11 @@ public class ContentSignatures
         /// <returns>A list of plots - each plot is the minute by minute scores for a single template.</returns>
         public static List<Plot> ContentDescriptionOfMultipleRecordingFiles(FileInfo listOfIndexFiles, FileInfo templatesFile)
         {
-            // Read in all template manifests
-            //var templates = Yaml.Deserialize<TemplateManifest[]>(templatesFile);
+            // total length in minutes of all the recordings
+            const int totalMinutesDurationOverAllRecordings = 1440;
+            const int startMinute = 0;
+
+            // Read in all the prepared templates
             var templates = Json.Deserialize<TemplateManifest[]>(templatesFile);
             var templatesAsDictionary = DataProcessing.ExtractDictionaryOfTemplateDictionaries(templates);
 
@@ -67,7 +70,8 @@ public static List<Plot> ContentDescriptionOfMultipleRecordingFiles(FileInfo lis
             // cycle through the directories
             for (int i = 0; i < filePaths.Count; i++)
             {
-                // read the spectral indices for the current file
+                // read the spectral indices for the current file.
+                //IMPORTANT: This method returns normalised index values
                 var dictionaryOfRecordingIndices = DataProcessing.ReadIndexMatrices(filePaths[i]);
 
                 // Draw the index matrices for check/debug purposes
@@ -79,11 +83,11 @@ public static List<Plot> ContentDescriptionOfMultipleRecordingFiles(FileInfo lis
                 completeListOfResults.AddRange(results);
 
                 // calculate the elapsed minutes in this recording
-                var matrix = dictionaryOfRecordingIndices["ENT"];
+                var matrix = dictionaryOfRecordingIndices.FirstValue();
                 elapsedMinutes += matrix.GetLength(0);
             }
 
-            var plotDict = DataProcessing.ConvertResultsToPlots(completeListOfResults, 1440, 0);
+            var plotDict = DataProcessing.ConvertResultsToPlots(completeListOfResults, totalMinutesDurationOverAllRecordings, startMinute);
             var contentPlots = DataProcessing.ConvertPlotDictionaryToPlotList(plotDict);
 
             // convert scores to z-scores
@@ -124,6 +128,14 @@ public static List<DescriptionResult> AnalyzeMinutes(
             return results;
         }
 
+        /// <summary>
+        /// IMPORTANT: The indices passed in the dictionary "oneMinuteOfIndices" must be normalised.
+        /// </summary>
+        /// <param name="templates">The templates read from json file.</param>
+        /// <param name="templatesAsDictionary">The numerical pasrt of each template.</param>
+        /// <param name="oneMinuteOfIndices">The normalised values of the indices derived from one minute of recording.</param>
+        /// <param name="minuteId">The minute ID, i.e. its temporal position.</param>
+        /// <returns>A single instance of a DescriptionResult.</returns>
         public static DescriptionResult AnalyzeOneMinute(
             TemplateManifest[] templates,
             Dictionary<string, Dictionary<string, double[]>> templatesAsDictionary,

src/AudioAnalysisTools/ContentDescriptionTools/DataProcessing.cs

@@ -32,6 +32,7 @@ public static Dictionary<string, TemplateManifest> ConvertTemplateArrayToDiction
 
         /// <summary>
         /// Reads in all the index matrices whose keys are in the above array of IndexNames.
+        /// Returns normalised values.
         /// </summary>
         /// <param name="filePath">Partial path to the index files.</param>
         /// <returns>a Dictionary of matrices containing normalised index values.</returns>
@@ -346,13 +347,13 @@ public static double[] GetFreqBinVector(Dictionary<string, double[]> dictionary,
         /// Converts individual results to a dictionary of plots.
         /// </summary>
         /// <param name="results">a list of results for each content type in every minute.</param>
-        /// <param name="arrayLength">The plot length will the total number of minutes scanned, typically 1440 or one day.</param>
+        /// <param name="arrayLength">The plot length will the total number of minutes scanned, typically 1440 for one day.</param>
         /// <param name="arrayStart">time start.</param>
-        public static Dictionary<string, double[]> ConvertResultsToArrays(List<DescriptionResult> results, int arrayLength, int arrayStart)
+        public static Dictionary<string, double[]> ConvertResultsToDictionaryOfArrays(List<DescriptionResult> results, int arrayLength, int arrayStart)
         {
             var arrays = new Dictionary<string, double[]>();
 
-            foreach (DescriptionResult result in results)
+            foreach (var result in results)
             {
                 var time = (int)Math.Round(result.StartTimeInCurrentRecordingFile.TotalMinutes);
                 var dict = result.GetDescriptionDictionary();
@@ -383,26 +384,30 @@ public static Dictionary<string, double[]> ConvertResultsToArrays(List<Descripti
         /// <param name="plotStart">time start.</param>
         public static Dictionary<string, Plot> ConvertResultsToPlots(List<DescriptionResult> results, int plotLength, int plotStart)
         {
+            var dictOfArrays = ConvertResultsToDictionaryOfArrays(results, plotLength, plotStart);
             var plots = new Dictionary<string, Plot>();
 
-            foreach (DescriptionResult result in results)
+            foreach (var kvp in dictOfArrays)
             {
-                var time = (int)Math.Round(result.StartTimeInCurrentRecordingFile.TotalMinutes);
-                var dict = result.GetDescriptionDictionary();
-                foreach (KeyValuePair<string, double> kvp in dict)
-                {
-                    var name = kvp.Key;
-                    var value = kvp.Value;
+                var name = kvp.Key;
+                var value = kvp.Value;
+                var plot = new Plot(name, value, 0.25); // NOTE: The threshold can be changed later.
+                plots.Add(name, plot);
+            }
 
-                    if (!plots.ContainsKey(name))
-                    {
-                        var scores = new double[plotLength];
-                        var plot = new Plot(name, scores, 0.25); // NOTE: The threshold can be changed later.
-                        plots.Add(name, plot);
-                    }
+            return plots;
+        }
 
-                    plots[name].data[plotStart + time] = value;
-                }
+        public static Dictionary<string, Plot> ConvertArraysToPlots(Dictionary<string, double[]> dictOfArrays, double threshold)
+        {
+            var plots = new Dictionary<string, Plot>();
+
+            foreach (var kvp in dictOfArrays)
+            {
+                var name = kvp.Key;
+                var value = kvp.Value;
+                var plot = new Plot(name, value, threshold);
+                plots.Add(name, plot);
             }
 
             return plots;

src/TowseyLibrary/FileTools.cs

@@ -335,6 +335,38 @@ public static void WriteDictionaryToFile(Dictionary<string, double[]> dictionary
             WriteTextFile(fPath, text.ToString());
         }
 
+        /// <summary>
+        /// Write a dictionary of arrays as a csv file where dictionary keys are column headers and the
+        /// arrays are the column entries.
+        /// WARNING: Assume that all arrays are of the same size!.
+        /// </summary>
+        /// <param name="dictionary">a dictionary of arrays of double.</param>
+        /// <param name="fPath">The file path.</param>
+        public static void WriteDictionaryAsCsvFile(Dictionary<string, double[]> dictionary, string fPath)
+        {
+            var kvp1 = dictionary.First();
+            var arrayLength = kvp1.Value.Length;
+
+            // set up an array of lines with first line for headers
+            var lines = new string[arrayLength + 1];
+
+            // now build up the lines
+            foreach (KeyValuePair<string, double[]> kvp in dictionary)
+            {
+                // add in the header
+                lines[0] += kvp.Key + ",";
+
+                // now add in values
+                var array = kvp.Value;
+                for (int i = 0; i < array.Length; i++)
+                {
+                    lines[i + 1] += $"{array[i]:F3}, ";
+                }
+            }
+
+            WriteTextFile(fPath, lines);
+        }
+
         public static void Append2TextFile(string fPath, string line)
         {
             bool saveExistingFile = false;

src/TowseyLibrary/Plot.cs

@@ -137,11 +137,19 @@ public Image DrawAnnotatedPlot(int height)
             // var font = new Font(family, 10, FontStyle.Regular, GraphicsUnit.Pixel);
             var font = new Font("Tahoma", 9);
             var g = Graphics.FromImage(image);
-            g.DrawString(this.title, font, Brushes.Red, new PointF(10, 0));
+            g.DrawString(this.title, font, Brushes.Red, new PointF(8, 0));
+
+            if (this.data.Length > 500)
+            {
+                g.DrawString(this.title, font, Brushes.Red, new PointF(length - 80, 0));
+            }
+
+            if (this.data.Length > 1200)
+            {
+                // ReSharper disable once PossibleLossOfFraction
+                g.DrawString(this.title, font, Brushes.Red, new PointF(length / 2, 0));
+            }
 
-            // ReSharper disable once PossibleLossOfFraction
-            g.DrawString(this.title, font, Brushes.Red, new PointF(length / 2, 0));
-            g.DrawString(this.title, font, Brushes.Red, new PointF(length - 80, 0));
             return image;
         }