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Complete removal of Dev methods
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Closes #139

Dev methods were an oddity that never should have occurred. They are removed.
However, since @towsey encoded a lot of valuable information as comments in these files, I've done my best to move all the dev method contents into a `Dev.md` text file that can be referred to until this encoded knowledge is transferred to a better location.
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@atruskie
atruskie committed Feb 17, 2018
1 parent 8cc6596 commit acfd88b
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Showing 43 changed files with 1,236 additions and 2,960 deletions.
11 changes: 0 additions & 11 deletions src/AnalysisPrograms/AED.cs
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Expand Up @@ -215,12 +215,6 @@ public static AcousticEvent[] CallAed(BaseSonogram sonogram, AedConfiguration ae
return events;
}

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
public static Arguments Dev(object obj)
{
throw new NotImplementedException();
}

public static Image DrawSonogram(BaseSonogram sonogram, IEnumerable<AcousticEvent> events)
{
var image = new Image_MultiTrack(sonogram.GetImage(false, true));
Expand All @@ -240,11 +234,6 @@ public static Image DrawSonogram(BaseSonogram sonogram, IEnumerable<AcousticEven

public static void Execute(Arguments arguments)
{
if (arguments == null)
{
arguments = Dev(arguments);
}

TowseyLibrary.Log.Verbosity = 1;
string date = "# DATE AND TIME: " + DateTime.Now;
LoggedConsole.WriteLine("# Running acoustic event detection.");
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548 changes: 0 additions & 548 deletions src/AnalysisPrograms/AcousticIndices - Copy.cs
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This file was deleted.

84 changes: 0 additions & 84 deletions src/AnalysisPrograms/AcousticIndices.cs
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Expand Up @@ -58,90 +58,6 @@ public class AcousticIndices : IAnalyser2
public string Description
=> "Generates all our default acoustic indices, including summary indices and spectral indices. Also generates false color spectrograms IFF IndexCalculationDuration==60.0";

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
public static void Dev(object arguments)
{
if (arguments == null)
{
arguments = new object();

//string recordingPath = @"C:\SensorNetworks\WavFiles\Human\Planitz.wav";
//string configPath = @"C:\SensorNetworks\Output\AcousticIndices\Indices.cfg";
//string outputDir = @"C:\SensorNetworks\Output\AcousticIndices\";
//string csvPath = @"C:\SensorNetworks\Output\AcousticIndices\AcousticIndices.csv";

string recordingPath = @"C:\SensorNetworks\WavFiles\SunshineCoast\DM420036_min407.wav";
string configPath = @"C:\SensorNetworks\Software\AudioAnalysis\AnalysisConfigFiles\Towsey.Acoustic.cfg";
string outputDir = @"C:\SensorNetworks\Output\SunshineCoast\Site1\Towsey.Acoustic";
string csvPath = @"C:\SensorNetworks\Output\SunshineCoast\Site1\Towsey.Acoustic\DM420036_min407_Towsey.Acoustic.Indices.csv";

//string recordingPath = @"C:\SensorNetworks\WavFiles\Crows\Crows111216-001Mono5-7min.mp3";
//string configPath = @"C:\SensorNetworks\Output\SunshineCoast\Site1\Towsey.Acoustic\temp.cfg";
//string outputDir = @"C:\SensorNetworks\Output\Crow\";
//string csvPath = @"C:\SensorNetworks\Output\Crow\Towsey.Acoustic.Indices.csv";

string title = "# FOR EXTRACTION OF Acoustic Indices";
string date = "# DATE AND TIME: " + DateTime.Now;
LoggedConsole.WriteLine(title);
LoggedConsole.WriteLine(date);
LoggedConsole.WriteLine("# Output folder: " + outputDir);
LoggedConsole.WriteLine("# Recording file: " + Path.GetFileName(recordingPath));

int startMinute = 0;
int durationSeconds = 0; //set zero to get entire recording
var tsStart = new TimeSpan(0, startMinute, 0); //hours, minutes, seconds
var tsDuration = new TimeSpan(0, 0, durationSeconds); //hours, minutes, seconds
var segmentFileStem = Path.GetFileNameWithoutExtension(recordingPath);
var segmentFName = string.Format("{0}_{1}min.wav", segmentFileStem, startMinute);

//var sonogramFname = string.Format("{0}_{1}min.png", segmentFileStem, startMinute);
//var eventsFname = string.Format("{0}_{1}min.{2}.Events.csv", segmentFileStem, startMinute, "Towsey." + AnalysisName);
var indicesFname = string.Format("{0}_{1}min.{2}.Indices.csv", segmentFileStem, startMinute, "Towsey." + AnalysisName);

// if (true)
// {
// // task_ANALYSE
// arguments.Task = TaskAnalyse;
// arguments.Source = recordingPath.ToFileInfo();
// arguments.Config = configPath.ToFileInfo();
// arguments.Output = outputDir.ToDirectoryInfo();
// arguments.TmpWav = segmentFName;
// arguments.Indices = indicesFname;
// arguments.Start = (int?)tsStart.TotalSeconds;
// arguments.Duration = (int?)tsDuration.TotalSeconds;
// }
//
// if (false)
// {
// // task_LOAD_CSV
// ////string indicesImagePath = "some path or another";
// arguments.Task = TaskLoadCsv;
// arguments.InputCsv = csvPath.ToFileInfo();
// arguments.Config = configPath.ToFileInfo();
// }
//
// string indicesPath = Path.Combine(arguments.Output.FullName, arguments.Indices);
// FileInfo fiCsvIndices = new FileInfo(indicesPath);
// if (!fiCsvIndices.Exists)
// {
// Log.InfoFormat(
// "\n\n\n############\n WARNING! Indices CSV file not returned from analysis of minute {0} of file <{1}>.",
// arguments.Start,
// arguments.Source.FullName);
// }
// else
// {
// LoggedConsole.WriteLine("\n");
// DataTable dt = CsvTools.ReadCSVToTable(indicesPath, true);
// DataTableTools.WriteTable2Console(dt);
// }
//
// LoggedConsole.WriteLine("\n\n# Finished analysis:- " + arguments.Source.FullName);
}

return;
}

public void BeforeAnalyze(AnalysisSettings analysisSettings)
{
var configuration = (AcousticIndicesConfig)analysisSettings.Configuration;
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1 change: 0 additions & 1 deletion src/AnalysisPrograms/AnalysisPrograms.csproj
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Expand Up @@ -261,7 +261,6 @@
<Compile Include="AudioCutter.cs" />
<Compile Include="AudioFileCheck.cs" />
<Compile Include="Draw\Zooming\DrawZoomingSpectrograms.Arguments.cs" />
<Compile Include="Draw\Zooming\DrawZoomingSpectrograms.Dev.cs" />
<Compile Include="EventStatistics\EventStatisticsEntry.Arguments.cs" />
<Compile Include="EventStatistics\EventStatisticsAnalysis.cs" />
<Compile Include="EventStatistics\EventStatisticsEntry.cs" />
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32 changes: 0 additions & 32 deletions src/AnalysisPrograms/Audio2InputForConvCNN.cs
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Expand Up @@ -62,33 +62,6 @@ public override Task<int> Execute(CommandLineApplication app)
}
}

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
private static Arguments Dev()
{
DateTime time = DateTime.Now;
string datestamp = $"{time.Year}{time.Month:d2}{time.Day:d2}";
return new Arguments
{
// prior to processing
// Y:\Results\2014Aug29-000000 - ConvDNN Data Export\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.csv
// audio_event_id audio_recording_id audio_recording_uuid event_created_at_utc projects site_id site_name event_start_date_utc event_start_seconds event_end_seconds event_duration_seconds low_frequency_hertz high_frequency_hertz padding_start_time_seconds padding_end_time_seconds common_tags species_tags other_tags listen_url library_url

// Y:\Results\2014Aug29-000000 - ConvDNN Data Export\Output\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv
// audio_event_id audio_recording_id audio_recording_uuid event_created_at_utc projects site_id site_name event_start_date_utc event_start_seconds event_end_seconds event_duration_seconds low_frequency_hertz high_frequency_hertz padding_start_time_seconds padding_end_time_seconds common_tags species_tags other_tags listen_url library_url path download_success skipped

// csv file containing recording info, call bounds etc
//Source = @"C:\SensorNetworks\Output\ConvDNN\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\ConvDNNData\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv".ToFileInfo(),
Source = @"Y:\Results\2014Aug29-000000 - Mangalam Data Export\Output\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv".ToFileInfo(),

Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Mangalam.Sonogram.yml",

Output = (@"C:\SensorNetworks\Output\ConvDNN\" + datestamp).ToDirectoryInfo(),
};

//throw new NoDeveloperMethodException();
}

/// <summary>
/// This is the entrypoint for generating ConCNN spectrograms - one at a time
/// </summary>
Expand Down Expand Up @@ -144,11 +117,6 @@ public static void Main(Arguments arguments)
// set preprocessing parameter
bool doPreprocessing = true;

if (arguments == null)
{
arguments = Dev();
}

var output = arguments.Output;
if (!output.Exists)
{
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42 changes: 0 additions & 42 deletions src/AnalysisPrograms/Audio2Sonogram.cs
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Expand Up @@ -69,50 +69,8 @@ public override Task<int> Execute(CommandLineApplication app)
}
}

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
private static Arguments Dev()
{
return new Arguments
{
//MARINE
//Source = @"C:\SensorNetworks\WavFiles\MarineRecordings\20130318_171500.wav".ToFileInfo(),
//Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.SonogramMarine.yml".ToFileInfo(),
//Output = @"C:\SensorNetworks\Output\MarineSonograms\".ToDirectoryInfo(),

// LEWINs RAIL
//Source = @"C:\SensorNetworks\WavFiles\LewinsRail\BAC2_20071008-062040.wav".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\LewinsRail\BAC1_20071008-081607.wav".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\LewinsRail\BAC2_20071008-085040.wav".ToFileInfo(),
//Output = @"C:\SensorNetworks\Output\LewinsRail".ToDirectoryInfo(),
Source = @"G:\SensorNetworks\WavFiles\LewinsRail\FromLizZnidersic\Lewinsrail_TasmanIs_Tractor_SM304253_0151119_0640_1min.wav".ToFileInfo(),
Output = @"C:\SensorNetworks\Output\LewinsRail\LewinsRail_ThreeCallTypes".ToDirectoryInfo(),

//CANETOAD
//Source = @"Y:\Canetoad\FromPaulRoe\canetoad_CubberlaCreek_100529_16bitPCM.wav".ToFileInfo(),

//Source = @"C:\SensorNetworks\WavFiles\Frogs\JCU\Litoria fellax1.mp3".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\Frogs\MiscillaneousDataSet\CaneToads_rural1_20_MONO.wav".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\TestRecordings\NW_NW273_20101013-051200-0514-1515-Brown Cuckoo-dove1.wav".ToFileInfo(),

//Source = @"C:\SensorNetworks\WavFiles\ConvDNNData\Kanowski_651_233394_20120831_072112_4.0__.wav".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\ConvDNNData\Melaleuca_Middle_183_192469_20101123_013009_4.0__.wav".ToFileInfo(),
//Source = @"C:\SensorNetworks\WavFiles\ConvDNNData\SE_399_188293_20101014_132950_4.0__.wav".ToFileInfo(),

Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Sonogram.yml",

//Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Mangalam.Sonogram.yml".ToFileInfo(),
};

throw new NoDeveloperMethodException();
}

public static void Main(Arguments arguments)
{
if (arguments == null)
{
arguments = Dev();
}

// 1. set up the necessary files
FileInfo sourceRecording = arguments.Source;
FileInfo configFile = arguments.Config.ToFileInfo();
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76 changes: 0 additions & 76 deletions src/AnalysisPrograms/CanetoadOld_OBSOLETE.cs
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Expand Up @@ -100,82 +100,6 @@ public override string Identifier

#region Public Methods and Operators

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
public static void Dev(Arguments arguments)
{
bool executeDev = arguments == null;
if (executeDev)
{
arguments = new Arguments();
const string RecordingPath =
//@"C:\SensorNetworks\WavFiles\Canetoad\FromPaulRoe\canetoad_CubberlaCreek_100529_16bitPCM.wav";
//@"Y:\Canetoad\FromPaulRoe\canetoad_CubberlaCreek_100529_16bitPCM.wav";
//@"C:\SensorNetworks\WavFiles\Canetoad\020313.MP3\Towsey.CanetoadOld\020313_608min.wav";
//@"C:\SensorNetworks\WavFiles\Canetoad\020313.MP3\Towsey.CanetoadOld\020313_619min.wav";
//@"Y:\Results\2014Nov11-083640 - Towsey.Canetoad JCU Campus Test 020313\JCU\Campus\020313.MP3\Towsey.CanetoadOld\020313_619min.wav";
//@"Y:\Results\2014Nov11-083640 - Towsey.Canetoad JCU Campus Test 020313\JCU\Campus\020313.MP3\Towsey.CanetoadOld\020313_375min.wav"; // 42, 316,375,422,704
//@"Y:\Results\2014Nov11-083640 - Towsey.Canetoad JCU Campus Test 020313\JCU\Campus\020313.MP3\Towsey.CanetoadOld\020313_297min.wav";
//@"F:\SensorNetworks\WavFiles\CaneToad\CaneToad Release Call 270213-8.wav";
@"F:\SensorNetworks\WavFiles\CaneToad\UndetectedCalls-2014\KiyomiUndetected210214-1.mp3";

//string recordingPath = @"C:\SensorNetworks\WavFiles\Canetoad\FromPaulRoe\canetoad_CubberlaCreek_100530_2_16bitPCM.wav";
//string recordingPath = @"C:\SensorNetworks\WavFiles\Canetoad\FromPaulRoe\canetoad_CubberlaCreek_100530_1_16bitPCM.wav";
//string recordingPath = @"C:\SensorNetworks\WavFiles\Canetoad\RuralCanetoads_9Jan\toads_rural_9jan2010\toads_rural1_16.mp3";
const string ConfigPath =
@"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Canetoad.yml";
const string OutputDir = @"C:\SensorNetworks\Output\Frogs\Canetoad\";

////string csvPath = @"C:\SensorNetworks\Output\Test\TEST_Indices.csv";
string title = "# FOR DETECTION OF CANETOAD using DCT OSCILLATION DETECTION";
string date = "# DATE AND TIME: " + DateTime.Now;
LoggedConsole.WriteLine(title);
LoggedConsole.WriteLine(date);
LoggedConsole.WriteLine("# Output folder: " + OutputDir);
LoggedConsole.WriteLine("# Recording file: " + Path.GetFileName(RecordingPath));

TowseyLibrary.Log.Verbosity = 1;
const int StartMinute = 0;
const int DurationSeconds = 0; // set zero to get entire recording
TimeSpan start = TimeSpan.FromMinutes(StartMinute); // hours, minutes, seconds
TimeSpan duration = TimeSpan.FromSeconds(DurationSeconds); // hours, minutes, seconds
string segmentFileStem = Path.GetFileNameWithoutExtension(RecordingPath);
string segmentFName = string.Format("{0}_{1}min.wav", segmentFileStem, StartMinute);
string sonogramFname = string.Format("{0}_{1}min.png", segmentFileStem, StartMinute);
string eventsFname = string.Format(
"{0}_{1}min.{2}.Events.csv",
segmentFileStem,
StartMinute,
"Towsey." + AnalysisName);
string indicesFname = string.Format(
"{0}_{1}min.{2}.Indices.csv",
segmentFileStem,
StartMinute,
"Towsey." + AnalysisName);

if (true)
{
arguments.Source = RecordingPath.ToFileInfo();
arguments.Config = ConfigPath.ToFileInfo();
arguments.Output = OutputDir.ToDirectoryInfo();
arguments.Start = start.TotalSeconds;
arguments.Duration = duration.TotalSeconds;
}

if (false)
{
// loads a csv file for visualisation
////string indicesImagePath = "some path or another";
////var fiCsvFile = new FileInfo(restOfArgs[0]);
////var fiConfigFile = new FileInfo(restOfArgs[1]);
////var fiImageFile = new FileInfo(restOfArgs[2]); //path to which to save image file.
////IAnalysis analyser = new AnalysisTemplate();
////var dataTables = analyser.ProcessCsvFile(fiCsvFile, fiConfigFile);
////returns two datatables, the second of which is to be converted to an image (fiImageFile) for display
}
}

Execute(arguments);
}

/// <summary>
/// A WRAPPER AROUND THE analyzer.Analyze(analysisSettings) METHOD
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19 changes: 0 additions & 19 deletions src/AnalysisPrograms/Create4Sonograms.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -50,27 +50,8 @@ public override Task<int> Execute(CommandLineApplication app)
}
}

[Obsolete("See https://github.com/QutBioacoustics/audio-analysis/issues/134")]
private static Arguments Dev()
{
return new Arguments
{
//Source = @"C:\SensorNetworks\WavFiles\LewinsRail\BAC1_20071008-081607.wav".ToFileInfo(),
//Output = @"C:\SensorNetworks\Output\Sonograms\BAC1_20071008-081607.png".ToFileInfo(),
Source = @"C:\SensorNetworks\WavFiles\TestRecordings\BAC\BAC2_20071008-085040.wav".ToFileInfo(),
Output = @"C:\SensorNetworks\Output\Sonograms\BAC2Sonograms\BAC2_20071008-085040.png",
Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Towsey.Sonogram.yml",
};

//throw new NoDeveloperMethodException();
}

public static void Main(Arguments arguments)
{
if (arguments == null)
{
arguments = Dev();
}

//1. set up the necessary files
//DirectoryInfo diSource = arguments.Source.Directory;
Expand Down
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