Fix up ContentSignatures.cs

Issue #252 Rework methods in ContentSignatures.cs inorder to be consistent with methods in ContentDescription.cs.

src/AnalysisPrograms/Sandpit.cs

@@ -64,11 +64,11 @@ public override Task<int> Execute(CommandLineApplication app)
                 Log.WriteLine("# Start Time = " + tStart.ToString(CultureInfo.InvariantCulture));
 
                 // CONTENT DESCRIPTION
-                //ContentDescriptionCreateTemplates();
-                //ContentDescriptionApplyTemplates();
+                ContentDescriptionCreateTemplates();
+                ContentDescriptionApplyTemplates();
 
                 //AnalyseFrogDataSet();
-                Audio2CsvOverOneFile();
+                //Audio2CsvOverOneFile();
                 //Audio2CsvOverMultipleFiles();
 
                 // used to get files from availae for Black rail and Least Bittern papers.
@@ -123,7 +123,7 @@ public override Task<int> Execute(CommandLineApplication app)
         public static void ContentDescriptionCreateTemplates()
         {
             var templateManifests = new FileInfo(@"C:\Ecoacoustics\ContentDescription\ContentDescriptionTemplateManifests.yml");
-            var templateDefinitions = new FileInfo(@"C:\Ecoacoustics\ContentDescription\TemplateDefinitions.json");
+            var templateDefinitions = new FileInfo(@"C:\Ecoacoustics\ContentDescription\Towsey.TemplateDefinitions.json");
             TemplateManifest.CreateNewFileOfTemplateDefinitions(templateManifests, templateDefinitions);
             Console.WriteLine("# Finished creation of new manifest");
         }
@@ -132,20 +132,29 @@ public static void ContentDescriptionApplyTemplates()
         {
             Console.WriteLine("# Start scanning with content description templates");
 
-            var templatesFile = new FileInfo(@"C:\Ecoacoustics\ContentDescription\TemplateDefinitions.json");
-            var listOfIndexFiles = new FileInfo(@"C:\Ecoacoustics\Output\Test\Test24HourRecording\TasmanIslandMezIndexFiles.txt");
-            var contentPlots = AudioAnalysisTools.ContentDescriptionTools.ContentSignatures.ContentDescriptionOfMultipleRecordingFiles(listOfIndexFiles, templatesFile);
+            var templatesFile = new FileInfo(@"C:\Ecoacoustics\ContentDescription\Towsey.TemplateDefinitions.json");
+            var listOfIndexFiles = new FileInfo(Path.Combine(@"C:\Ecoacoustics\Output\Test\Test24HourRecording", "TasmanIslandMezIndexFiles.txt"));
+            var dataDirectory = @"C:\Ecoacoustics\Output\Test\Test24HourRecording";
+            var outputDirectory = @"C:\Ecoacoustics\ContentDescription";
 
+            var contentDictionary = ContentSignatures.ContentDescriptionOfMultipleRecordingFiles(listOfIndexFiles, templatesFile);
+
+            // Write the results to a csv file
+            var filePath = Path.Combine(outputDirectory, "AcousticSignatures.csv");
+            FileTools.WriteDictionaryAsCsvFile(contentDictionary, filePath);
+
+            // get content description plots and use to examine score distributions.
+            var contentPlots = ContentSignatures.GetPlots(contentDictionary);
             var images = GraphsAndCharts.DrawPlotDistributions(contentPlots);
             var plotsImage = ImageTools.CombineImagesVertically(images);
-            var path1 = Path.Combine(@"C:\Ecoacoustics\ContentDescription", "ScoreDistributions.png");
+            var path1 = Path.Combine(outputDirectory, "ScoreDistributions.png");
             plotsImage.Save(path1);
 
-            // Attach content description plots to LDFC spectrogram and write to file
-            var path = Path.Combine(@"C:\Ecoacoustics\Output\Test\Test24HourRecording", "Testing__2Maps.png");
+            // Attach plots to LDFC spectrogram and write to file
+            var path = Path.Combine(dataDirectory, "Testing__2Maps.png");
             var ldfcSpectrogram = Image.FromFile(path);
             var image = ContentVisualization.DrawLdfcSpectrogramWithContentScoreTracks(ldfcSpectrogram, contentPlots);
-            var path2 = Path.Combine(@"C:\Ecoacoustics\ContentDescription", "Testing_2Maps.CONTENTnew07.png");
+            var path2 = Path.Combine(outputDirectory, "Testing_2Maps.CONTENTnew07.png");
             image.Save(path2);
             Console.WriteLine("# Finished scanning recording with content description templates");
         }

src/AudioAnalysisTools/ContentDescriptionTools/ContentSignatures.cs

@@ -47,10 +47,9 @@ public class ContentSignatures
         /// <param name="listOfIndexFiles">A text file, each line being the path to the acoustic indices derived from one recording.</param>
         /// <param name="templatesFile">A json file containing an array of acoustic templates.</param>
         /// <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)
+        public static Dictionary<string, double[]> ContentDescriptionOfMultipleRecordingFiles(FileInfo listOfIndexFiles, FileInfo templatesFile)
         {
-            // total length in minutes of all the recordings
-            const int totalMinutesDurationOverAllRecordings = 1440;
+            // ASSUMPTION: 
             const int startMinute = 0;
 
             // Read in all the prepared templates
@@ -86,18 +85,9 @@ public static List<Plot> ContentDescriptionOfMultipleRecordingFiles(FileInfo lis
                 elapsedMinutes += matrix.GetLength(0);
             }
 
-            var plotDict = DataProcessing.ConvertResultsToPlots(completeListOfResults, totalMinutesDurationOverAllRecordings, startMinute);
-            var contentPlots = DataProcessing.ConvertPlotDictionaryToPlotList(plotDict);
-
-            // convert scores to z-scores
-            //contentPlots = DataProcessing.SubtractMeanPlusSd(contentPlots);
-
-            //the following did not work as well.
-            //contentPlots = DataProcessing.SubtractModeAndSd(contentPlots);
-
-            // Use percentile thresholding followed by normalize in 0,1.
-            contentPlots = DataProcessing.PercentileThresholding(contentPlots, 90);
-            return contentPlots;
+            // convert completeListOfResults to dictionary of score arrays
+            var contentDictionary = DataProcessing.ConvertResultsToDictionaryOfArrays(completeListOfResults, elapsedMinutes, startMinute);
+            return contentDictionary;
         }
 
         public static List<DescriptionResult> AnalyzeMinutes(
@@ -131,7 +121,7 @@ public static List<DescriptionResult> AnalyzeMinutes(
         /// 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="templatesAsDictionary">The numerical part 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>
@@ -182,5 +172,22 @@ public static DescriptionResult AnalyzeOneMinute(
 
             return descriptionResult;
         }
+
+        public 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
+            //contentPlots = DataProcessing.SubtractMeanPlusSd(contentPlots);
+
+            //the following did not work as well.
+            //contentPlots = DataProcessing.SubtractModeAndSd(contentPlots);
+
+            // Use percentile thresholding followed by normalize in 0,1.
+            contentPlots = DataProcessing.PercentileThresholding(contentPlots, 90);
+            return contentPlots;
+        }
     }
 }

src/AudioAnalysisTools/ContentDescriptionTools/TemplateManifest.cs

@@ -79,10 +79,11 @@ public static void CreateNewFileOfTemplateDefinitions(FileInfo manifestFile, Fil
                 }
             }
 
-            var templatesFilePath = Path.Combine(manifestFile.DirectoryName ?? throw new InvalidOperationException(), "TemplateDefinitions.json");
+            var templatesFileName = templateDefinitionsFile.Name;
+            var templatesFilePath = Path.Combine(manifestFile.DirectoryName ?? throw new InvalidOperationException(), templatesFileName);
 
             // Save the previous templates file
-            string backupTemplatesFilePath = Path.Combine(manifestFile.DirectoryName, "TemplateDefinitions.Backup.json");
+            string backupTemplatesFilePath = Path.Combine(manifestFile.DirectoryName, templatesFileName + ".Backup.json");
             if (File.Exists(backupTemplatesFilePath))
             {
                 File.Delete(backupTemplatesFilePath);