private int Execute(Arguments arguments)
{
var errors = new List <string>();
Log.Info("Checking required executables and libraries can be found and loaded");
// this is an important call used in analyze long recordings.
// This call effectively check is we can load types and if files are present (I think)
try
{
AnalysisCoordinator.GetAnalyzers <IAnalyser2>(typeof(MainEntry).Assembly);
}
catch (ReflectionTypeLoadException rtlex)
{
errors.Add(ExceptionLookup.FormatReflectionTypeLoadException(rtlex, true));
}
// master audio utility checks for available executables
try
{
var utility = new MasterAudioUtility();
}
catch (Exception ex)
{
errors.Add(ex.Message);
}
if (MainEntry.CheckForDataAnnotations() is string message)
{
errors.Add(message);
}
Type type = Type.GetType("Mono.Runtime");
if (type != null)
{
errors.Add($"We no longer use Mono with ${Meta.Name}. DO NOT prefix the {Meta.Name} prefix with `mono`.");
}
// don't have much more to check at the current time
if (errors.Count == 0)
{
Log.Success("Valid environment");
return(ExceptionLookup.Ok);
}
else
{
foreach (var error in errors)
{
Log.Error(error);
}
// not using exception lookup on purpose - it's static constructor loads more types
return(ExceptionLookup.UnhandledExceptionErrorCode);
}
}
public void TestNamedDirectoryWorksWithSubFolders()
{
var analyzer = new DummyAnalyzer(false);
var settings = analyzer.DefaultSettings;
settings.AnalysisOutputDirectory = this.TestOutputDirectory;
var actual = AnalysisCoordinator.GetNamedDirectory(settings.AnalysisOutputDirectory, analyzer, "a", "b", "c");
var expected = this.TestOutputDirectory.Combine("Ecosounds.TempusSubstitutus/a/b/c");
Assert.AreEqual(expected.FullName, actual.FullName);
}
private StringBuilder GetAnalyzersTable()
{
var analysers = AnalysisCoordinator
.GetAnalyzers <IAnalyser2>(typeof(MainEntry).Assembly)
.OrderBy(x => x.Identifier)
.ToArray();
const string identifier = "Identifier";
var indentifierWidth = Math.Max(identifier.Length, analysers.Max((analyser2) => analyser2.Identifier.Length)) + 1;
var typeLength = 16 + 1;
int bufferWidth;
try
{
bufferWidth = Console.BufferWidth;
}
catch (Exception)
{
bufferWidth = 80;
}
var consoleWidth = Math.Max((10 * (bufferWidth / 10)) - Environment.NewLine.Length, 80);
var descrptionLength = consoleWidth - indentifierWidth - typeLength;
string tableFormat = "{0, " + -indentifierWidth + "}{1, " + -typeLength + "}{2," + -descrptionLength + "}";
string header = string.Format(tableFormat, identifier, "Type", "Description");
StringBuilder table = new StringBuilder((analysers.Length + 3) * consoleWidth);
table.AppendLine(header);
table.AppendLine(string.Empty.PadRight(header.Length, '-'));
foreach (IAnalyser2 analyser in analysers)
{
var isEventRecognizer = analyser is IEventRecognizer;
var description = analyser.Description;
if (string.IsNullOrWhiteSpace(description))
{
description = "<No description>";
}
if (description.Length > descrptionLength)
{
description = description.WordWrap(descrptionLength, indentifierWidth + typeLength);
}
table.AppendLine(string.Format(tableFormat, analyser.Identifier, isEventRecognizer ? "Event Recognizer" : "Type unknown", description));
}
return(table);
}
private AnalysisResult2[] TestAnalysisCoordinator(ISegment <FileInfo>[] segments)
{
Contract.Requires(segments != null);
var preparer = new DummySourcePreparer();
AnalysisCoordinator coordinator = new AnalysisCoordinator(
preparer,
saveIntermediateWavFiles: SaveBehavior.Always,
uniqueDirectoryPerSegment: false,
isParallel: false);
IAnalyser2 dummyAnalyzer = new DummyAnalyzer(false);
var settings = dummyAnalyzer.DefaultSettings;
settings.AnalysisOutputDirectory = this.TestOutputDirectory;
settings.AnalysisTempDirectory = this.TestOutputDirectory.Combine("Temp");
return(coordinator.Run(segments, dummyAnalyzer, settings));
}
public static T FindAndCheckAnalyzer <T>(string analysisIdentifier, string partialIdentifier)
where T : class, IAnalyser2
{
string searchName;
if (analysisIdentifier.IsNotWhitespace())
{
searchName = analysisIdentifier;
Log.Debug($"Searching for exact analysis identifier name {searchName} (from a CLI option)");
}
else
{
// split name (e.g. "Towsey.Acoustics.Zooming.yml") on periods
var fragments = partialIdentifier.Split(new[] { "." }, StringSplitOptions.RemoveEmptyEntries);
Contract.Requires <CommandLineArgumentException>(
fragments.Length >= 2,
$"We need at least two segments to search for an analyzer, supplied name `{partialIdentifier}` is insufficient.");
// assume identifier (e.g. "Towsey.Acoustic") in first two segments
searchName = fragments[0] + "." + fragments[1];
Log.Debug($"Searching for partial analysis identifier name. `{searchName}` extracted from `{partialIdentifier}`");
}
var analyzers = AnalysisCoordinator.GetAnalyzers <T>(typeof(MainEntry).Assembly).ToList();
T analyzer = analyzers.FirstOrDefault(a => a.Identifier == searchName);
if (analyzer == null)
{
var error = $"We cannot determine what analysis you want to run. We tried to search for \"{searchName}\"";
LoggedConsole.WriteErrorLine(error);
var knownAnalyzers = analyzers.Aggregate(string.Empty, (a, i) => a + $" {i.Identifier}\n");
LoggedConsole.WriteLine("Available analyzers are:\n" + knownAnalyzers);
throw new ValidationException($"Cannot find an IAnalyser2 with the name `{searchName}`");
}
Log.Info($"Using analyzer {analyzer.Identifier}");
return(analyzer);
}
public void SummariseResults(AnalysisSettings settings, FileSegment inputFileSegment, EventBase[] events, SummaryIndexBase[] indices, SpectralIndexBase[] spectralIndices, AnalysisResult2[] results)
{
var acousticIndicesConfig = (AcousticIndicesConfig)settings.AnalysisAnalyzerSpecificConfiguration;
var sourceAudio = inputFileSegment.Source;
var resultsDirectory = AnalysisCoordinator.GetNamedDirectory(settings.AnalysisOutputDirectory, this);
bool tileOutput = acousticIndicesConfig.TileOutput;
var frameWidth = acousticIndicesConfig.FrameLength;
int sampleRate = AppConfigHelper.DefaultTargetSampleRate;
sampleRate = acousticIndicesConfig.ResampleRate ?? sampleRate;
// Gather settings for rendering false color spectrograms
var ldSpectrogramConfig = acousticIndicesConfig.LdSpectrogramConfig;
string basename = Path.GetFileNameWithoutExtension(sourceAudio.Name);
// output to disk (so other analyzers can use the data,
// only data - configuration settings that generated these indices
// this data can then be used by post-process analyses
/* NOTE: The value for FrameStep is used only when calculating a standard spectrogram
* FrameStep is NOT used when calculating Summary and Spectral indices.
*/
var indexConfigData = new IndexGenerationData()
{
RecordingExtension = inputFileSegment.Source.Extension,
RecordingBasename = basename,
RecordingStartDate = inputFileSegment.TargetFileStartDate,
RecordingDuration = inputFileSegment.TargetFileDuration.Value,
SampleRateOriginal = inputFileSegment.TargetFileSampleRate.Value,
SampleRateResampled = sampleRate,
FrameLength = frameWidth,
FrameStep = settings.Configuration.GetIntOrNull(AnalysisKeys.FrameStep) ?? frameWidth,
IndexCalculationDuration = acousticIndicesConfig.IndexCalculationDurationTimeSpan,
BgNoiseNeighbourhood = acousticIndicesConfig.BgNoiseBuffer,
AnalysisStartOffset = inputFileSegment.SegmentStartOffset ?? TimeSpan.Zero,
MaximumSegmentDuration = settings.AnalysisMaxSegmentDuration,
BackgroundFilterCoeff = SpectrogramConstants.BACKGROUND_FILTER_COEFF,
LongDurationSpectrogramConfig = ldSpectrogramConfig,
};
var icdPath = FilenameHelpers.AnalysisResultPath(
resultsDirectory,
basename,
IndexGenerationData.FileNameFragment,
"json");
Json.Serialise(icdPath.ToFileInfo(), indexConfigData);
// gather spectra to form spectrograms. Assume same spectra in all analyzer results
// this is the most efficient way to do this
// gather up numbers and strings store in memory, write to disk one time
// this method also AUTOMATICALLY SORTS because it uses array indexing
var dictionaryOfSpectra = spectralIndices.ToTwoDimensionalArray(SpectralIndexValues.CachedSelectors, TwoDimensionalArray.Rotate90ClockWise);
// Calculate the index distribution statistics and write to a json file. Also save as png image
var indexDistributions = IndexDistributions.WriteSpectralIndexDistributionStatistics(dictionaryOfSpectra, resultsDirectory, basename);
// HACK: do not render false color spectrograms unless IndexCalculationDuration = 60.0 (the normal resolution)
if (acousticIndicesConfig.IndexCalculationDurationTimeSpan != 60.0.Seconds())
{
Log.Warn("False color spectrograms were not rendered");
}
else
{
FileInfo indicesPropertiesConfig = acousticIndicesConfig.IndexPropertiesConfig.ToFileInfo();
// Actually draw false color / long duration spectrograms
Tuple <Image <Rgb24>, string>[] images =
LDSpectrogramRGB.DrawSpectrogramsFromSpectralIndices(
inputDirectory: resultsDirectory,
outputDirectory: resultsDirectory,
ldSpectrogramConfig: ldSpectrogramConfig,
indexPropertiesConfigPath: indicesPropertiesConfig,
indexGenerationData: indexConfigData,
basename: basename,
analysisType: this.Identifier,
indexSpectrograms: dictionaryOfSpectra,
indexStatistics: indexDistributions,
imageChrome: (!tileOutput).ToImageChrome());
if (tileOutput)
{
Debug.Assert(images.Length == 2);
Log.Info("Tiling output at scale: " + acousticIndicesConfig.IndexCalculationDuration);
foreach (var image in images)
{
TileOutput(resultsDirectory, Path.GetFileNameWithoutExtension(sourceAudio.Name), image.Item2 + ".Tile", inputFileSegment, image.Item1);
}
}
}
}
/// <summary>
/// 2. Analyses long audio recording (mp3 or wav) as per passed config file. Outputs an events.csv file AND an
/// indices.csv file
/// Signed off: Michael Towsey 4th December 2012
/// </summary>
public static void Execute(Arguments arguments)
{
if (arguments == null)
{
throw new NoDeveloperMethodException();
}
LoggedConsole.WriteLine("# PROCESS LONG RECORDING");
LoggedConsole.WriteLine("# DATE AND TIME: " + DateTime.Now);
// 1. set up the necessary files
var sourceAudio = arguments.Source;
var configFile = arguments.Config.ToFileInfo();
var outputDirectory = arguments.Output;
var tempFilesDirectory = arguments.TempDir;
// if a temp dir is not given, use output dir as temp dir
if (tempFilesDirectory == null)
{
Log.Warn("No temporary directory provided, using output directory");
tempFilesDirectory = outputDirectory;
}
// try an automatically find the config file
if (configFile == null)
{
throw new FileNotFoundException("No config file argument provided");
}
else if (!configFile.Exists)
{
Log.Warn($"Config file {configFile.FullName} not found... attempting to resolve config file");
// we use .ToString() here to get the original input string - Using fullname always produces an absolute path wrt to pwd... we don't want to prematurely make asusmptions:
// e.g. We require a missing absolute path to fail... that wouldn't work with .Name
// e.g. We require a relative path to try and resolve, using .FullName would fail the first absolute check inside ResolveConfigFile
configFile = ConfigFile.Resolve(configFile.ToString(), Directory.GetCurrentDirectory().ToDirectoryInfo());
}
if (arguments.StartOffset.HasValue ^ arguments.EndOffset.HasValue)
{
throw new InvalidStartOrEndException("If StartOffset or EndOffset is specified, then both must be specified");
}
if (arguments.StartOffset.HasValue && arguments.EndOffset.HasValue && arguments.EndOffset.Value <= arguments.StartOffset.Value)
{
throw new InvalidStartOrEndException("Start offset must be less than end offset.");
}
LoggedConsole.WriteLine("# Recording file: " + sourceAudio.FullName);
LoggedConsole.WriteLine("# Configuration file: " + configFile);
LoggedConsole.WriteLine("# Output folder: " + outputDirectory);
LoggedConsole.WriteLine("# Temp File Directory: " + tempFilesDirectory);
// optionally copy logs / config to make results easier to understand
// TODO: remove, see https://github.com/QutEcoacoustics/audio-analysis/issues/133
if (arguments.WhenExitCopyConfig || arguments.WhenExitCopyLog)
{
AppDomain.CurrentDomain.ProcessExit += (sender, args) => { Cleanup(arguments, configFile); };
}
// 2. initialize the analyzer
// we're changing the way resolving config files works. Ideally, we'd like to use statically typed config files
// but we can't do that unless we know which type we have to load first! Currently analyzer to load is in
// the config file so we can't know which analyzer we can use. Thus we will change to using the file name,
// or an argument to resolve the analyzer to load.
// Get analysis name:
IAnalyser2 analyzer = FindAndCheckAnalyzer <IAnalyser2>(arguments.AnalysisIdentifier, configFile.Name);
// 2. get the analysis config
AnalyzerConfig configuration = analyzer.ParseConfig(configFile);
SaveBehavior saveIntermediateWavFiles = configuration.SaveIntermediateWavFiles;
bool saveIntermediateDataFiles = configuration.SaveIntermediateCsvFiles;
SaveBehavior saveSonogramsImages = configuration.SaveSonogramImages;
bool filenameDate = configuration.RequireDateInFilename;
if (configuration[AnalysisKeys.AnalysisName].IsNotWhitespace())
{
Log.Warn("Your config file has `AnalysisName` set - this property is deprecated and ignored");
}
// AT 2018-02: changed logic so default index properties loaded if not provided
FileInfo indicesPropertiesConfig = IndexProperties.Find(configuration, configFile);
if (indicesPropertiesConfig == null || !indicesPropertiesConfig.Exists)
{
Log.Warn("IndexProperties config can not be found! Loading a default");
indicesPropertiesConfig = ConfigFile.Default <Dictionary <string, IndexProperties> >();
}
LoggedConsole.WriteLine("# IndexProperties Cfg: " + indicesPropertiesConfig.FullName);
// min score for an acceptable event
Log.Info("Minimum event threshold has been set to " + configuration.EventThreshold);
FileSegment.FileDateBehavior defaultBehavior = FileSegment.FileDateBehavior.Try;
if (filenameDate)
{
if (!FileDateHelpers.FileNameContainsDateTime(sourceAudio.Name))
{
throw new InvalidFileDateException(
"When RequireDateInFilename option is set, the filename of the source audio file must contain "
+ "a valid AND UNAMBIGUOUS date. Such a date was not able to be parsed.");
}
defaultBehavior = FileSegment.FileDateBehavior.Required;
}
// 3. initilize AnalysisCoordinator class that will do the analysis
var analysisCoordinator = new AnalysisCoordinator(
new LocalSourcePreparer(),
saveIntermediateWavFiles,
false,
arguments.Parallel);
// 4. get the segment of audio to be analysed
// if tiling output, specify that FileSegment needs to be able to read the date
var fileSegment = new FileSegment(sourceAudio, arguments.AlignToMinute, null, defaultBehavior);
var bothOffsetsProvided = arguments.StartOffset.HasValue && arguments.EndOffset.HasValue;
if (bothOffsetsProvided)
{
fileSegment.SegmentStartOffset = TimeSpan.FromSeconds(arguments.StartOffset.Value);
fileSegment.SegmentEndOffset = TimeSpan.FromSeconds(arguments.EndOffset.Value);
}
else
{
Log.Debug("Neither start nor end segment offsets provided. Therefore both were ignored.");
}
// 6. initialize the analysis settings object
var analysisSettings = analyzer.DefaultSettings;
analysisSettings.ConfigFile = configFile;
analysisSettings.Configuration = configuration;
analysisSettings.AnalysisOutputDirectory = outputDirectory;
analysisSettings.AnalysisTempDirectory = tempFilesDirectory;
analysisSettings.AnalysisDataSaveBehavior = saveIntermediateDataFiles;
analysisSettings.AnalysisImageSaveBehavior = saveSonogramsImages;
analysisSettings.AnalysisChannelSelection = arguments.Channels;
analysisSettings.AnalysisMixDownToMono = arguments.MixDownToMono;
var segmentDuration = configuration.SegmentDuration?.Seconds();
if (!segmentDuration.HasValue)
{
segmentDuration = analysisSettings.AnalysisMaxSegmentDuration ?? TimeSpan.FromMinutes(1);
Log.Warn(
$"Can't read `{nameof(AnalyzerConfig.SegmentDuration)}` from config file. "
+ $"Default value of {segmentDuration} used)");
}
analysisSettings.AnalysisMaxSegmentDuration = segmentDuration.Value;
var segmentOverlap = configuration.SegmentOverlap?.Seconds();
if (!segmentOverlap.HasValue)
{
segmentOverlap = analysisSettings.SegmentOverlapDuration;
Log.Warn(
$"Can't read `{nameof(AnalyzerConfig.SegmentOverlap)}` from config file. "
+ $"Default value of {segmentOverlap} used)");
}
analysisSettings.SegmentOverlapDuration = segmentOverlap.Value;
// set target sample rate
var resampleRate = configuration.ResampleRate;
if (!resampleRate.HasValue)
{
resampleRate = analysisSettings.AnalysisTargetSampleRate ?? AppConfigHelper.DefaultTargetSampleRate;
Log.Warn(
$"Can't read {nameof(configuration.ResampleRate)} from config file. "
+ $"Default value of {resampleRate} used)");
}
analysisSettings.AnalysisTargetSampleRate = resampleRate;
Log.Info(
$"{nameof(configuration.SegmentDuration)}={segmentDuration}, "
+ $"{nameof(configuration.SegmentOverlap)}={segmentOverlap}, "
+ $"{nameof(configuration.ResampleRate)}={resampleRate}");
// 7. ####################################### DO THE ANALYSIS ###################################
LoggedConsole.WriteLine("START ANALYSIS ...");
var analyserResults = analysisCoordinator.Run(fileSegment, analyzer, analysisSettings);
// ##############################################################################################
// 8. PROCESS THE RESULTS
LoggedConsole.WriteLine(string.Empty);
LoggedConsole.WriteLine("START PROCESSING RESULTS ...");
if (analyserResults == null)
{
LoggedConsole.WriteErrorLine("###################################################\n");
LoggedConsole.WriteErrorLine("The Analysis Run Coordinator has returned a null result.");
LoggedConsole.WriteErrorLine("###################################################\n");
throw new AnalysisOptionDevilException();
}
// Merge and correct main result types
EventBase[] mergedEventResults = ResultsTools.MergeResults(analyserResults, ar => ar.Events, ResultsTools.CorrectEvent);
SummaryIndexBase[] mergedIndicesResults = ResultsTools.MergeResults(analyserResults, ar => ar.SummaryIndices, ResultsTools.CorrectSummaryIndex);
SpectralIndexBase[] mergedSpectralIndexResults = ResultsTools.MergeResults(analyserResults, ar => ar.SpectralIndices, ResultsTools.CorrectSpectrumIndex);
// not an exceptional state, do not throw exception
if (mergedEventResults != null && mergedEventResults.Length == 0)
{
LoggedConsole.WriteWarnLine("The analysis produced no EVENTS (mergedResults had zero count)");
}
if (mergedIndicesResults != null && mergedIndicesResults.Length == 0)
{
LoggedConsole.WriteWarnLine("The analysis produced no Summary INDICES (mergedResults had zero count)");
}
if (mergedSpectralIndexResults != null && mergedSpectralIndexResults.Length == 0)
{
LoggedConsole.WriteWarnLine("The analysis produced no Spectral INDICES (merged results had zero count)");
}
// 9. CREATE SUMMARY INDICES IF NECESSARY (FROM EVENTS)
#if DEBUG
// get the duration of the original source audio file - need this to convert Events datatable to Indices Datatable
var audioUtility = new MasterAudioUtility(tempFilesDirectory);
var mimeType = MediaTypes.GetMediaType(sourceAudio.Extension);
var sourceInfo = audioUtility.Info(sourceAudio);
// updated by reference all the way down in LocalSourcePreparer
Debug.Assert(fileSegment.TargetFileDuration == sourceInfo.Duration);
#endif
var duration = fileSegment.TargetFileDuration.Value;
ResultsTools.ConvertEventsToIndices(
analyzer,
mergedEventResults,
ref mergedIndicesResults,
duration,
configuration.EventThreshold);
int eventsCount = mergedEventResults?.Length ?? 0;
int numberOfRowsOfIndices = mergedIndicesResults?.Length ?? 0;
// 10. Allow analysers to post-process
// TODO: remove results directory if possible
var instanceOutputDirectory =
AnalysisCoordinator.GetNamedDirectory(analysisSettings.AnalysisOutputDirectory, analyzer);
// 11. IMPORTANT - this is where IAnalyser2's post processor gets called.
// Produces all spectrograms and images of SPECTRAL INDICES.
// Long duration spectrograms are drawn IFF analysis type is Towsey.Acoustic
analyzer.SummariseResults(analysisSettings, fileSegment, mergedEventResults, mergedIndicesResults, mergedSpectralIndexResults, analyserResults);
// 12. SAVE THE RESULTS
string fileNameBase = Path.GetFileNameWithoutExtension(sourceAudio.Name);
var eventsFile = ResultsTools.SaveEvents(analyzer, fileNameBase, instanceOutputDirectory, mergedEventResults);
var indicesFile = ResultsTools.SaveSummaryIndices(analyzer, fileNameBase, instanceOutputDirectory, mergedIndicesResults);
var spectraFile = ResultsTools.SaveSpectralIndices(analyzer, fileNameBase, instanceOutputDirectory, mergedSpectralIndexResults);
// 13. THIS IS WHERE SUMMARY INDICES ARE PROCESSED
// Convert summary indices to black and white tracks image
if (mergedIndicesResults == null)
{
Log.Info("No summary indices produced");
}
else
{
if (indicesPropertiesConfig == null || !indicesPropertiesConfig.Exists)
{
throw new InvalidOperationException("Cannot process indices without an index configuration file, the file could not be found!");
}
// this arbitrary amount of data.
if (mergedIndicesResults.Length > 5000)
{
Log.Warn("Summary Indices Image not able to be drawn - there are too many indices to render");
}
else
{
var basename = Path.GetFileNameWithoutExtension(fileNameBase);
string imageTitle = $"SOURCE:{basename}, {Meta.OrganizationTag}; ";
// Draw Tracks-Image of Summary indices
// set time scale resolution for drawing of summary index tracks
TimeSpan timeScale = TimeSpan.FromSeconds(0.1);
Bitmap tracksImage =
IndexDisplay.DrawImageOfSummaryIndices(
IndexProperties.GetIndexProperties(indicesPropertiesConfig),
indicesFile,
imageTitle,
timeScale,
fileSegment.TargetFileStartDate);
var imagePath = FilenameHelpers.AnalysisResultPath(instanceOutputDirectory, basename, "SummaryIndices", ImageFileExt);
tracksImage.Save(imagePath);
}
}
// 14. wrap up, write stats
LoggedConsole.WriteLine("INDICES CSV file(s) = " + (indicesFile?.Name ?? "<<No indices result, no file!>>"));
LoggedConsole.WriteLine("\tNumber of rows (i.e. minutes) in CSV file of indices = " + numberOfRowsOfIndices);
LoggedConsole.WriteLine(string.Empty);
if (eventsFile == null)
{
LoggedConsole.WriteLine("An Events CSV file was NOT returned.");
}
else
{
LoggedConsole.WriteLine("EVENTS CSV file(s) = " + eventsFile.Name);
LoggedConsole.WriteLine("\tNumber of events = " + eventsCount);
}
Log.Success($"Analysis Complete.\nSource={sourceAudio.Name}\nOutput={instanceOutputDirectory.FullName}");
}
public static async Task <int> ExecuteAsync(Arguments arguments)
{
Log.Info("Event statistics analysis begin");
// validate arguments
var input = arguments.Source;
var config = arguments.Config.ToFileInfo();
if (!input.Exists)
{
throw new FileNotFoundException("Cannot find source file", input.FullName);
}
// try an automatically find the config file
if (config == null)
{
throw new FileNotFoundException("No config file argument provided");
}
else if (!config.Exists)
{
Log.Warn($"Config file {config.FullName} not found... attempting to resolve config file");
// we use the original input string - Using FileInfo fullname always produces an
// absolute path relative to pwd... we don't want to prematurely make assumptions:
// e.g. We require a missing absolute path to fail... that wouldn't work with .Name
// e.g. We require a relative path to try and resolve, using .FullName would fail the first absolute
// check inside ResolveConfigFile
config = ConfigFile.Resolve(arguments.Config, Directory.GetCurrentDirectory().ToDirectoryInfo());
}
// if a temp dir is not given, use output dir as temp dir
if (arguments.TempDir == null)
{
Log.Warn("No temporary directory provided, using backup directory");
}
// Remote: create an instance of our API helpers
IApi api = arguments.WorkbenchApi.IsNullOrEmpty() ? Api.Default : Api.Parse(arguments.WorkbenchApi);
// log some helpful messages
Log.Info("Events file: " + input);
Log.Info("Configuration file: " + config);
Log.Info("Output folder: " + arguments.Output);
Log.Info("Temp File Directory: " + arguments.TempDir);
Log.Info("Api: " + api);
// Remote: Test we can log in to the workbench
var auth = new AuthenticationService(api);
Task <IAuthenticatedApi> task;
if (arguments.AuthenticationToken.IsNotWhitespace())
{
Log.Debug("Using token for authentication");
task = auth.CheckLogin(arguments.AuthenticationToken);
}
else
{
var username = LoggedConsole.Prompt("Enter your username or email for the acoustic workbench:");
var password = LoggedConsole.Prompt("Enter your password for the acoustic workbench:", forPassword: true);
task = auth.Login(username, password);
//task = auth.Login("*****@*****.**", "tsettest");
}
LoggedConsole.WriteWaitingLine(task, "Logging into workbench...");
var authenticatedApi = await task.TimeoutAfter(Service.ClientTimeout).ConfigureAwait(false);
Log.Info("Login success" + authenticatedApi);
// read events/annotation file
Log.Info("Now reading input data");
// Read events from provided CSV file.
// Also tag them with an order index to allow sorting in the same order as they were provided to us.
var events = Csv
.ReadFromCsv <ImportedEvent>(input, throwOnMissingField: false)
.Select(
(x, i) =>
{
x.Order = i;
return(x);
})
.ToArray();
if (events.Length == 0)
{
Log.Warn("No events imported - source file empty. Exiting");
return(ExceptionLookup.NoData);
}
Log.Info($"Events read, {events.Length} read.");
// need to validate the events
var invalidEvents = events.Where(e => !e.IsValid()).ToArray();
if (invalidEvents.Length > 0)
{
throw new InvalidOperationException(
"Invalid event detected."
+ $" {invalidEvents.Length} events are not valid. The first invalid event is {invalidEvents[0]}");
}
// next gather meta data for all events
// and transform list of events into list of segments
// NOTE: to save on I/O sometimes if events share the same audio block, then multiple events will be
// bundled into the same analysis segment.
var resolver = new EventMetadataResolver(
authenticatedApi,
PaddingFunction,
arguments.Parallel ? 25 : 1);
var metadataTask = resolver.GetRemoteMetadata(events);
// wait for 1 second per event - this should be an order of magnitude greater than what is needed
ISegment <AudioRecording>[] segments = await metadataTask.TimeoutAfter(events.Length);
Log.Info($"Metadata collected, preparing to start analysis");
// finally time to start preparing jobs
ISourcePreparer preparer = new RemoteSourcePreparer(authenticatedApi, allowSegmentcutting: false);
AnalysisCoordinator coordinator = new AnalysisCoordinator(
preparer,
SaveBehavior.Never,
uniqueDirectoryPerSegment: false,
isParallel: arguments.Parallel);
// instantiate the Analysis
EventStatisticsAnalysis analysis = new EventStatisticsAnalysis();
// derserialize the config file
var configuration = analysis.ParseConfig(config);
AnalysisSettings settings = analysis.DefaultSettings;
settings.AnalysisOutputDirectory = arguments.Output;
settings.AnalysisTempDirectory = arguments.TempDir;
settings.Configuration = configuration;
var results = coordinator.Run(segments, analysis, settings);
var allEvents = results.SelectMany(es => es.Events).ToArray();
var eventsWithErrors = allEvents.Count(x => ((EventStatistics)x).Error);
if (eventsWithErrors > 0)
{
Log.Warn($"Errors occurred when calculating statistics for {eventsWithErrors} events.");
}
Log.Trace("Sorting event statistics results");
Array.Sort(allEvents);
Log.Info("Executing summary");
// TODO: implement if needed
analysis.SummariseResults(settings, null, allEvents, null, null, results);
Log.Debug("Summary complete");
var instanceOutputDirectory =
AnalysisCoordinator.GetNamedDirectory(settings.AnalysisOutputDirectory, analysis);
var resultName = FilenameHelpers.AnalysisResultPath(
instanceOutputDirectory,
input,
analysis.Identifier,
"csv");
// NOTE: we are only saving event files
Log.Info($"Writing results to {resultName}");
analysis.WriteEventsFile(resultName.ToFileInfo(), allEvents.AsEnumerable());
Log.Debug("Writing events completed");
var summaryStats = new
{
numberEvents = allEvents.Length,
durationEvents = allEvents.Sum(x => ((EventStatistics)x).EventDurationSeconds),
numberRecordings = allEvents.Select(x => ((EventStatistics)x).AudioRecordingId).Distinct().Count(),
durationAudioProcessed = results.Sum(x => x.SegmentAudioDuration.TotalSeconds),
remoteAudioDownloaded = (preparer as RemoteSourcePreparer)?.TotalBytesRecieved,
};
Log.Info("Summary statistics:\n" + Json.SerializeToString(summaryStats));
Log.Success("Event statistics analysis complete!");
return(ExceptionLookup.Ok);
}
private void TestAnalysisCoordinatorPaths(SaveBehavior wav, bool unique, DirectoryInfo temp, State[] states)
{
Contract.Requires(states.Length == 5);
var preparer = new DummySourcePreparer();
AnalysisCoordinator coordinator = new AnalysisCoordinator(
preparer,
saveIntermediateWavFiles: wav,
uniqueDirectoryPerSegment: unique,
isParallel: false);
// an empty non-existent file
var source = TempFileHelper.NewTempFile(this.TestOutputDirectory).Touch();
FileSegment segment = new FileSegment(source, duration: 120.0.Seconds(), sampleRate: 123456);
var dummyAnalyzer = new DummyAnalyzer(true);
var settings = dummyAnalyzer.DefaultSettings;
Trace.WriteLine("Class output directory:" + this.TestOutputDirectory.FullName);
settings.AnalysisMaxSegmentDuration = 60.Seconds();
settings.AnalysisOutputDirectory = this.AnalysisOutput;
settings.AnalysisTempDirectory = temp;
this.settingsAccessor.Fields["fallbackTempDirectory"]?.SetValue(settings, this.FallbackTemp.FullName);
var task = Task.Run(() =>
{
var results = coordinator.Run(segment, dummyAnalyzer, settings);
// summarize is currently called manually
dummyAnalyzer.SummariseResults(settings, segment, null, null, null, results);
});
// set up path strings
string basename = Path.GetFileNameWithoutExtension(source.Name);
var paths = new CoordinatorPathTestSet
{
output = this.AnalysisOutput.FullName,
temp = (temp ?? this.TestTemp).FullName,
tempNull = this.FallbackTemp.FullName,
fragment = "Ecosounds.TempusSubstitutus",
unique1 = basename + "_000000.00-000060.00",
unique2 = basename + "_000060.00-000120.00",
source = basename,
};
// wait for the analyzer to pause
while (!dummyAnalyzer.IsPaused)
{
Thread.Sleep(0);
}
// manually pump the analysis
// before analyze
this.AssertFilesAreAsExpected(0, states[0], paths);
dummyAnalyzer.Pump();
// segment 1
this.AssertFilesAreAsExpected(1, states[1], paths);
dummyAnalyzer.Pump();
// segment 2
this.AssertFilesAreAsExpected(2, states[2], paths);
dummyAnalyzer.Pump();
// after summarize
this.AssertFilesAreAsExpected(3, states[3], paths);
// complete
// TODO: remove this rubbish and stick in a IoC file system for testing!
dummyAnalyzer.Pump(false);
do
{
Thread.Sleep(0.5.Seconds());
dummyAnalyzer.Pump(false);
}while (!task.IsCompleted);
task.Wait(1.0.Seconds());
this.AssertFilesAreAsExpected(4, states[4], paths);
Assert.IsTrue(task.IsCompleted, "task was not yet completed");
}
private int Execute(Arguments arguments)
{
var errors = new List <string>();
Log.Info("Checking required executables and libraries can be found and loaded");
// this is an important call used in analyze long recordings.
// This call effectively check is we can load types and if files are present (I think)
try
{
AnalysisCoordinator.GetAnalyzers <IAnalyser2>(typeof(MainEntry).Assembly);
}
catch (ReflectionTypeLoadException rtlex)
{
errors.Add(ExceptionLookup.FormatReflectionTypeLoadException(rtlex, true));
}
// master audio utility checks for available executables
try
{
var utility = new MasterAudioUtility();
}
catch (Exception ex)
{
errors.Add(ex.Message);
}
if (MainEntry.CheckForDataAnnotations() is string message)
{
errors.Add(message);
}
if (AppConfigHelper.IsMono)
{
Type type = Type.GetType("Mono.Runtime");
if (type != null)
{
MethodInfo displayName = type.GetMethod("GetDisplayName", BindingFlags.NonPublic | BindingFlags.Static);
if (displayName?.Invoke(null, null) is string name)
{
var version = Regex.Match(name, @".*(\d+\.\d+\.\d+\.\d+).*").Groups[1].Value;
Console.WriteLine(version);
if (new Version(version) > new Version(5, 5))
{
Log.Success($"Your mono version {name} is greater than our required Mono version 5.5");
}
else
{
errors.Add($"Mono version is {name}, we require at least Mono 5.5");
}
}
else
{
errors.Add("Could not get Mono display name");
}
}
}
// don't have much more to check at the current time
if (errors.Count == 0)
{
Log.Success("Valid environment");
return(ExceptionLookup.Ok);
}
else
{
foreach (var error in errors)
{
Log.Error(error);
}
// not using exception lookup on purpose - it's static constructor loads more types
return(ExceptionLookup.UnhandledExceptionErrorCode);
}
}
public override void SummariseResults(
AnalysisSettings analysisSettings,
FileSegment inputFileSegment,
EventBase[] events,
SummaryIndexBase[] indices,
SpectralIndexBase[] spectralIndices,
AnalysisResult2[] results)
{
// below is example of how to access values in ContentDescription config file.
//sampleRate = analysisSettings.Configuration.GetIntOrNull(AnalysisKeys.ResampleRate) ?? sampleRate;
var cdConfiguration = (CdConfig)analysisSettings.Configuration;
var ldSpectrogramConfig = cdConfiguration.LdSpectrogramConfig;
//var cdConfigFile = analysisSettings.ConfigFile;
//var configDirectory = cdConfigFile.DirectoryName ?? throw new ArgumentNullException(nameof(cdConfigFile), "Null value");
var sourceAudio = inputFileSegment.Source;
string basename = Path.GetFileNameWithoutExtension(sourceAudio.Name);
var resultsDirectory = AnalysisCoordinator.GetNamedDirectory(analysisSettings.AnalysisOutputDirectory, this);
// check for null values - this was recommended by ReSharper!
if (inputFileSegment.TargetFileDuration == null || inputFileSegment.TargetFileSampleRate == null)
{
throw new NullReferenceException();
}
// output config data to disk so other analyzers can use the data,
// Should contain data only - i.e. the configuration settings that generated these indices
// this data can then be used by later analysis processes.
var indexConfigData = new IndexGenerationData()
{
RecordingExtension = inputFileSegment.Source.Extension,
RecordingBasename = basename,
RecordingStartDate = inputFileSegment.TargetFileStartDate,
RecordingDuration = inputFileSegment.TargetFileDuration.Value,
SampleRateOriginal = inputFileSegment.TargetFileSampleRate.Value,
SampleRateResampled = ContentSignatures.SampleRate,
FrameLength = ContentSignatures.FrameSize,
FrameStep = ContentSignatures.FrameSize,
IndexCalculationDuration = TimeSpan.FromSeconds(ContentSignatures.IndexCalculationDurationInSeconds),
BgNoiseNeighbourhood = TimeSpan.FromSeconds(5), // default value for content description
AnalysisStartOffset = inputFileSegment.SegmentStartOffset ?? TimeSpan.Zero,
MaximumSegmentDuration = analysisSettings.AnalysisMaxSegmentDuration,
BackgroundFilterCoeff = SpectrogramConstants.BACKGROUND_FILTER_COEFF,
LongDurationSpectrogramConfig = ldSpectrogramConfig,
};
var icdPath = FilenameHelpers.AnalysisResultPath(
resultsDirectory,
basename,
IndexGenerationData.FileNameFragment,
"json");
Json.Serialise(icdPath.ToFileInfo(), indexConfigData);
// gather spectra to form spectrograms. Assume same spectra in all analyzer results
var dictionaryOfSpectra = spectralIndices.ToTwoDimensionalArray(SpectralIndexValuesForContentDescription.CachedSelectors, TwoDimensionalArray.Rotate90ClockWise);
// Calculate the index distribution statistics and write to a json file. Also save as png image
// The following method returns var indexDistributions =, but we have no use for them.
IndexDistributions.WriteSpectralIndexDistributionStatistics(dictionaryOfSpectra, resultsDirectory, basename);
// Draw ldfc spectrograms and return path to 2maps image.
string ldfcSpectrogramPath =
DrawSpectrogramsFromSpectralIndices(
ldSpectrogramConfig,
outputDirectory: resultsDirectory,
indexGenerationData: indexConfigData,
basename: basename,
indexSpectrograms: dictionaryOfSpectra);
// Gather the content description results into an array of DescriptionResult and then convert to dictionary
var allContentDescriptionResults = results.Select(x => (DescriptionResult)x.MiscellaneousResults[nameof(DescriptionResult)]);
var contentDictionary = DataProcessing.ConvertResultsToDictionaryOfArrays(allContentDescriptionResults.ToList());
// Write the results to a csv file
var filePath = Path.Combine(resultsDirectory.FullName, "AcousticSignatures.csv");
// TODO: fix this so it writes header and a column of content description values.
//Csv.WriteToCsv(new FileInfo(filePath), contentDictionary);
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);
plotsImage.Save(Path.Combine(resultsDirectory.FullName, "DistributionsOfContentScores.png"));
// Attach content description plots to LDFC spectrogram and write to file
var ldfcSpectrogram = Image.Load <Rgb24>(ldfcSpectrogramPath);
var image = ContentVisualization.DrawLdfcSpectrogramWithContentScoreTracks(ldfcSpectrogram, contentPlots);
var path3 = Path.Combine(resultsDirectory.FullName, basename + ".ContentDescription.png");
image.Save(path3);
}