/// <summary>
/// ONLY Use this concatenation method when you want to concatenate the files for a fixed single day.
/// The files to be concatenated must be somewhere in the subdirectory structure of the passed list of data directories
/// Read them into a dictionary
/// MOST RECENT METHOD TO CONCATENATE Spectral INDEX.CSV FILES - Early September 2015.
/// It is designed to deal with Yvonne's case where want to concatenate files distributed over arbitrary directories.
/// It only merges files for the passed fixed date. i.e only 24 hours
/// </summary>
public static void DrawSpectralIndexFiles(
Dictionary <string, double[, ]> dictionary,
LdSpectrogramConfig sgConfig,
IndexGenerationData indexGenerationData,
FileInfo indexPropertiesConfigFileInfo,
DirectoryInfo opDir,
SiteDescription siteDescription,
FileInfo sunriseDataFile = null,
List <GapsAndJoins> segmentErrors = null)
{
// derive new indices such as sqrt(PMN), NCDI etc -- main reason for this is to view what their distributions look like.
dictionary = IndexMatrices.AddDerivedIndices(dictionary);
// Calculate the index distribution statistics and write to a json file. Also save as png image
if (indexGenerationData.RecordingStartDate != null)
{
DateTimeOffset dto = (DateTimeOffset)indexGenerationData.RecordingStartDate;
string dateString = $"{dto.Year}{dto.Month:D2}{dto.Day:D2}";
string opFileStem = $"{siteDescription.SiteName}_{dateString}";
var indexDistributions = IndexDistributions.WriteSpectralIndexDistributionStatistics(dictionary, opDir, opFileStem);
//SummaryIndexBase[] summaryIndices = null;
string analysisType = "Towsey.Acoustic";
Tuple <Image, string>[] tuple = LDSpectrogramRGB.DrawSpectrogramsFromSpectralIndices(
opDir, // topLevelDirectories[0], // this should not be required but it is - because things have gotten complicated !
opDir,
sgConfig,
indexPropertiesConfigFileInfo,
indexGenerationData,
opFileStem,
analysisType,
dictionary,
null, //summaryIndices,
indexDistributions,
siteDescription,
sunriseDataFile,
segmentErrors,
ImageChrome.With);
}
}
public static void DrawStackOfZoomedSpectrograms(
DirectoryInfo inputDirectory,
DirectoryInfo outputDirectory,
AnalysisIoInputDirectory io,
ZoomParameters common,
string analysisTag,
TimeSpan focalTime,
int imageWidth)
{
var zoomConfig = common.SpectrogramZoomingConfig;
LdSpectrogramConfig ldsConfig = common.SpectrogramZoomingConfig.LdSpectrogramConfig;
//var distributions = common.IndexDistributions;
string fileStem = common.OriginalBasename;
var indexGeneration = common.IndexGenerationData;
TimeSpan dataScale = indexGeneration.IndexCalculationDuration;
// ####################### DERIVE ZOOMED OUT SPECTROGRAMS FROM SPECTRAL INDICES
//var indexGenerationData = common.IndexGenerationData;
var indexProperties = zoomConfig.IndexProperties;
var(spectra, filteredIndexProperties) = ZoomCommon.LoadSpectra(io, analysisTag, fileStem, zoomConfig.LdSpectrogramConfig, indexProperties);
Stopwatch sw = Stopwatch.StartNew();
// Set the default time-scales in seconds per pixel.
// These were changed on 3rd April 2019 to better match those in the current zooming config file.
double[] imageScales = { 60, 30, 15, 7.5, 3.2, 1.6, 0.8, 0.4, 0.2 };
if (zoomConfig.SpectralIndexScale != null)
{
imageScales = zoomConfig.SpectralIndexScale;
}
sw = Stopwatch.StartNew();
int scaleCount = imageScales.Length;
var imageList = new List <Image <Rgb24> >();
for (int i = 0; i < scaleCount; i++)
{
var imageScale = TimeSpan.FromSeconds(imageScales[i]);
var image = DrawIndexSpectrogramAtScale(ldsConfig, indexGeneration, filteredIndexProperties, focalTime, dataScale, imageScale, imageWidth, spectra, fileStem);
if (image != null)
{
imageList.Add(image);
string name = $"{fileStem}_FocalZoom_min{focalTime.TotalMinutes:f1}_scale{imageScales[i]}.png";
image.Save(Path.Combine(outputDirectory.FullName, name));
}
}
sw.Stop();
LoggedConsole.WriteLine("Finished spectrograms derived from spectral indices. Elapsed time = " + sw.Elapsed.TotalSeconds + " seconds");
// NOTE: The following code is deprecated. It was originally developed to provide some intermediate steps between the hi-resolution false-colour spectrograms
// and the standard grey scale spectrograms.
// ####################### DERIVE ZOOMED IN SPECTROGRAMS FROM STANDARD SPECTRAL FRAMES
/*
* int[] compressionFactor = { 8, 4, 2, 1 };
* int compressionCount = compressionFactor.Length;
* sw = Stopwatch.StartNew();
* double frameStepInSeconds = indexGeneration.FrameStep / (double)indexGeneration.SampleRateResampled;
* TimeSpan frameScale = TimeSpan.FromTicks((long)Math.Round(frameStepInSeconds * 10000000));
* if (zoomConfig.SpectralFrameScale != null)
* {
* imageScales = zoomConfig.SpectralFrameScale;
*
* // TODO: CONVERT IMAGE scales into Compression factors.
* compressionCount = imageScales.Length;
* compressionFactor = new int[compressionCount];
* compressionFactor[compressionCount - 1] = 1;
* double denom = imageScales[compressionCount - 1];
*
* for (int i = 0; i < compressionCount - 1; i++)
* {
* compressionFactor[i] = (int)Math.Round(imageScales[i] / denom);
* }
* }
*
* int maxCompression = compressionFactor[0];
* TimeSpan maxImageDuration = TimeSpan.FromTicks(maxCompression * imageWidth * frameScale.Ticks);
*
* TimeSpan halfMaxImageDuration = TimeSpan.FromMilliseconds(maxImageDuration.TotalMilliseconds / 2);
* TimeSpan startTimeOfMaxImage = TimeSpan.Zero;
* if (focalTime != TimeSpan.Zero)
* {
* startTimeOfMaxImage = focalTime - halfMaxImageDuration;
* }
*
* TimeSpan startTimeOfData = TimeSpan.FromMinutes(Math.Floor(startTimeOfMaxImage.TotalMinutes));
*
* List<double[]> frameData = ReadFrameData(inputDirectory, fileStem, startTimeOfMaxImage, maxImageDuration, zoomConfig, indexGeneration.MaximumSegmentDuration.Value);
*
* // get the index data to add into the
* // TimeSpan imageScale1 = TimeSpan.FromSeconds(0.1);
* double[,] indexData = spectra["PMN"];
*
* // make the images
* for (int i = 0; i < compressionCount; i++)
* {
* int factor = compressionFactor[i];
* var image = DrawFrameSpectrogramAtScale(ldsConfig, indexGeneration, startTimeOfData, factor, frameData, indexData, focalTime, frameScale, imageWidth);
* if (image != null)
* {
* imageList.Add(image);
* }
* }
*
* sw.Stop();
* LoggedConsole.WriteLine("Finished spectrograms derived from standard frames. Elapsed time = " + sw.Elapsed.TotalSeconds + " seconds");
*/
// combine the images into a stack
var combinedImage = ImageTools.CombineImagesVertically(imageList);
string fileName = $"{fileStem}_FocalZOOM_min{focalTime.TotalMinutes:f1}.png";
combinedImage.Save(Path.Combine(outputDirectory.FullName, fileName));
}
/// <summary>
/// This method can add in absolute time if you want.
/// Currently commented out - see below.
/// </summary>
public static Image <Rgb24> DrawIndexSpectrogramAtScale(
LdSpectrogramConfig config,
IndexGenerationData indexGenerationData,
Dictionary <string, IndexProperties> indexProperties,
TimeSpan focalTime,
TimeSpan dataScale,
TimeSpan imageScale,
int imageWidth,
Dictionary <string, double[, ]> spectra,
string basename)
{
if (spectra == null)
{
LoggedConsole.WriteLine("WARNING: NO SPECTRAL DATA SUPPLIED");
return(null);
}
// check that scalingFactor >= 1.0
double scalingFactor = Math.Round(imageScale.TotalMilliseconds / dataScale.TotalMilliseconds);
if (scalingFactor < 1.0)
{
LoggedConsole.WriteLine("WARNING: Scaling Factor < 1.0");
return(null);
}
Dictionary <string, IndexProperties> dictIp = indexProperties;
dictIp = InitialiseIndexProperties.FilterIndexPropertiesForSpectralOnly(dictIp);
// calculate start time by combining DatetimeOffset with minute offset.
TimeSpan sourceMinuteOffset = indexGenerationData.AnalysisStartOffset;
if (indexGenerationData.RecordingStartDate.HasValue)
{
DateTimeOffset dto = (DateTimeOffset)indexGenerationData.RecordingStartDate;
sourceMinuteOffset = dto.TimeOfDay + sourceMinuteOffset;
}
// calculate data duration from column count of abitrary matrix
var kvp = spectra.First();
var matrix = kvp.Value;
//var matrix = spectra["ACI"]; // assume this key will always be present!!
TimeSpan dataDuration = TimeSpan.FromSeconds(matrix.GetLength(1) * dataScale.TotalSeconds);
TimeSpan recordingStartTime = TimeSpan.Zero; // default = zero minute of day i.e. midnight
recordingStartTime = indexGenerationData.RecordingStartDate.Value.TimeOfDay.Add(indexGenerationData.AnalysisStartOffset);
TimeSpan offsetTime = TimeSpan.Zero;
TimeSpan imageDuration = TimeSpan.FromTicks(imageWidth * imageScale.Ticks);
TimeSpan halfImageDuration = TimeSpan.FromTicks(imageWidth * imageScale.Ticks / 2);
TimeSpan startTime = TimeSpan.Zero;
if (focalTime != TimeSpan.Zero)
{
startTime = focalTime - halfImageDuration;
}
if (startTime < TimeSpan.Zero)
{
offsetTime = TimeSpan.Zero - startTime;
startTime = TimeSpan.Zero;
}
TimeSpan endTime = imageDuration;
if (focalTime != TimeSpan.Zero)
{
endTime = focalTime + halfImageDuration;
}
if (endTime > dataDuration)
{
endTime = dataDuration;
}
TimeSpan spectrogramDuration = endTime - startTime;
int spectrogramWidth = (int)(spectrogramDuration.Ticks / imageScale.Ticks);
// get the plain unchromed spectrogram
var ldfcSpectrogram = ZoomCommon.DrawIndexSpectrogramCommon(
config,
indexGenerationData,
indexProperties,
startTime,
endTime,
dataScale,
imageScale,
imageWidth,
spectra,
basename);
if (ldfcSpectrogram == null)
{
LoggedConsole.WriteLine("WARNING: NO SPECTROGRAM AT SCALE " + imageScale);
return(null);
}
// now chrome spectrogram
ldfcSpectrogram.Mutate(g2 =>
{
// draw red line at focus time
if (focalTime != TimeSpan.Zero)
{
Pen pen = new Pen(Color.Red, 1);
TimeSpan focalOffset = focalTime - startTime;
int x1 = (int)(focalOffset.Ticks / imageScale.Ticks);
g2.DrawLine(pen, x1, 0, x1, ldfcSpectrogram.Height);
}
});
// draw the title bar
int nyquist = 22050 / 2; // default
if (indexGenerationData.SampleRateResampled > 0)
{
nyquist = indexGenerationData.SampleRateResampled / 2;
}
int herzInterval = 1000;
if (config != null)
{
herzInterval = config.YAxisTicInterval;
}
string title = $"SCALE={imageScale.TotalSeconds}s/px. Duration={spectrogramDuration} ";
//add chrome
// NEXT LINE USED ONLY IF WANT ABSOLUTE TIME
//startTime += recordingStartTime;
var titleBar = DrawTitleBarOfZoomSpectrogram(title, ldfcSpectrogram.Width);
ldfcSpectrogram = FrameZoomSpectrogram(
ldfcSpectrogram,
titleBar,
startTime,
imageScale,
config.XAxisTicInterval,
nyquist,
herzInterval);
// create the base canvas image on which to centre the focal image
var image = Drawing.NewImage(imageWidth, ldfcSpectrogram.Height, Color.DarkGray);
int xOffset = (int)(offsetTime.Ticks / imageScale.Ticks);
image.Mutate(g1 => g1.DrawImage(ldfcSpectrogram, new Point(xOffset, 0), 1));
return(image);
}
/// <summary>
/// This method can add in the absolute recording start time. However currently disabled.
/// </summary>
/// <param name="config">v.</param>
/// <param name="indexGenerationData">indexGenerationData.</param>
/// <param name="startTimeOfData">startTimeOfData.</param>
/// <param name="compressionFactor">compressionFactor.</param>
/// <param name="frameData">frameData.</param>
/// <param name="indexData">indexData.</param>
/// <param name="focalTime">focalTime.</param>
/// <param name="frameScale">frameScale.</param>
/// <param name="imageWidth">imageWidth.</param>
public static Image DrawFrameSpectrogramAtScale(
LdSpectrogramConfig config,
IndexGenerationData indexGenerationData,
TimeSpan startTimeOfData,
int compressionFactor,
List <double[]> frameData,
double[,] indexData,
TimeSpan focalTime,
TimeSpan frameScale,
int imageWidth)
{
if (frameData == null || frameData.Count == 0)
{
LoggedConsole.WriteLine("WARNING: NO SPECTRAL SPECTROGRAM DATA SUPPLIED");
return(null);
}
// var recordingStartTime = TimeSpan.Zero; // default = zero minute of day i.e. midnight
// var recordingStartTime = TimeTools.DateTimePlusTimeSpan(indexGenerationData.RecordingStartDate, indexGenerationData.AnalysisStartOffset);
TimeSpan imageScale = TimeSpan.FromTicks(frameScale.Ticks * compressionFactor);
TimeSpan imageDuration = TimeSpan.FromTicks(imageWidth * imageScale.Ticks);
TimeSpan halfImageDuration = TimeSpan.FromTicks(imageWidth * imageScale.Ticks / 2);
TimeSpan startTime = focalTime - halfImageDuration;
if (startTime < TimeSpan.Zero)
{
startTime = TimeSpan.Zero;
}
int startIndex = (int)((startTime.Ticks - startTimeOfData.Ticks) / frameScale.Ticks);
int requiredFrameCount = imageWidth * compressionFactor;
List <double[]> frameSelection = frameData.GetRange(startIndex, requiredFrameCount);
double[,] spectralSelection = MatrixTools.ConvertList2Matrix(frameSelection);
// compress spectrograms to correct scale
if (compressionFactor > 1)
{
spectralSelection = TemporalMatrix.CompressFrameSpectrograms(spectralSelection, compressionFactor);
}
var spectrogramImage = DrawStandardSpectrogramInFalseColour(spectralSelection);
int x1 = (int)(halfImageDuration.Ticks / imageScale.Ticks);
spectrogramImage.Mutate(g2 =>
{
// draw focus time on image
if (focalTime != TimeSpan.Zero)
{
Pen pen = new Pen(Color.Red, 1);
g2.DrawLine(pen, x1, 0, x1, spectrogramImage.Height);
}
});
int nyquist = 22050 / 2; // default
if (indexGenerationData.SampleRateResampled > 0)
{
nyquist = indexGenerationData.SampleRateResampled / 2;
}
int herzInterval = config.YAxisTicInterval;
string title = $"ZOOM SCALE={imageScale.TotalMilliseconds}ms/pixel Image duration={imageDuration} ";
var titleBar = DrawTitleBarOfZoomSpectrogram(title, spectrogramImage.Width);
// add the recording start time ONLY IF WANT ABSOLUTE TIME SCALE - obtained from info in file name
// startTime += recordingStartTime;
spectrogramImage = FrameZoomSpectrogram(spectrogramImage, titleBar, startTime, imageScale, config.XAxisTicInterval, nyquist, herzInterval);
// MAY WANT THESE CLIPPING TRACKS AT SOME POINT
// read high amplitude and clipping info into an image
//string indicesFile = Path.Combine(configuration.InputDirectoryInfo.FullName, fileStem + ".csv");
//string indicesFile = Path.Combine(config.InputDirectoryInfo.FullName, fileStem + ".Indices.csv");
//string indicesFile = Path.Combine(configuration.InputDirectoryInfo.FullName, fileStem + "_" + configuration.AnalysisType + ".csv");
//Image imageX = DrawSummaryIndices.DrawHighAmplitudeClippingTrack(indicesFile.ToFileInfo());
//if (null != imageX) imageX.Save(Path.Combine(outputDirectory.FullName, fileStem + ".ClipHiAmpl.png"));
// create the base image
Image image = new Image <Rgb24>(imageWidth, spectrogramImage.Height);
image.Mutate(g1 =>
{
g1.Clear(Color.DarkGray);
//int xOffset = (int)(startTime.Ticks / imageScale.Ticks);
int xOffset = (imageWidth / 2) - x1;
g1.DrawImage(spectrogramImage, new Point(xOffset, 0), 1);
});
return(image);
}
public static void DrawStackOfZoomedSpectrograms(DirectoryInfo inputDirectory, DirectoryInfo outputDirectory, ZoomParameters common, TimeSpan focalTime, int imageWidth, string analysisType)
{
var zoomConfig = common.SpectrogramZoomingConfig;
LdSpectrogramConfig ldsConfig = common.SpectrogramZoomingConfig.LdSpectrogramConfig;
var distributions = common.IndexDistributions;
var indexGeneration = common.IndexGenerationData;
string fileStem = common.OriginalBasename;
TimeSpan dataScale = indexGeneration.IndexCalculationDuration;
// ####################### DERIVE ZOOMED OUT SPECTROGRAMS FROM SPECTRAL INDICES
string[] keys = { "ACI", "BGN", "CVR", "DIF", "ENT", "EVN", "PMN", "POW", "RHZ", "RVT", "RPS", "RNG", "SUM", "SPT" };
var indexProperties = InitialiseIndexProperties.FilterIndexPropertiesForSpectralOnly(zoomConfig.IndexProperties);
Dictionary <string, double[, ]> spectra = IndexMatrices.ReadSpectralIndices(inputDirectory, fileStem, analysisType, keys);
Stopwatch sw = Stopwatch.StartNew();
// standard scales in seconds per pixel.
double[] imageScales = { 60, 24, 12, 6, 2, 1, 0.6, 0.2 };
if (zoomConfig.SpectralIndexScale != null)
{
imageScales = zoomConfig.SpectralIndexScale;
}
sw = Stopwatch.StartNew();
int scaleCount = imageScales.Length;
var imageList = new List <Image>();
for (int i = 0; i < scaleCount; i++)
{
var imageScale = TimeSpan.FromSeconds(imageScales[i]);
var image = DrawIndexSpectrogramAtScale(ldsConfig, indexGeneration, indexProperties, focalTime, dataScale, imageScale, imageWidth, spectra, fileStem);
if (image != null)
{
imageList.Add(image);
string name = $"{fileStem}_FocalZoom_min{focalTime.TotalMinutes:f1}_scale{imageScales[i]}.png";
image.Save(Path.Combine(outputDirectory.FullName, name));
}
}
sw.Stop();
LoggedConsole.WriteLine("Finished spectrograms derived from spectral indices. Elapsed time = " + sw.Elapsed.TotalSeconds + " seconds");
// ####################### DERIVE ZOOMED IN SPECTROGRAMS FROM STANDARD SPECTRAL FRAMES
int[] compressionFactor = { 8, 4, 2, 1 };
int compressionCount = compressionFactor.Length;
sw = Stopwatch.StartNew();
double frameStepInSeconds = indexGeneration.FrameStep / (double)indexGeneration.SampleRateResampled;
TimeSpan frameScale = TimeSpan.FromTicks((long)Math.Round(frameStepInSeconds * 10000000));
if (zoomConfig.SpectralFrameScale != null)
{
imageScales = zoomConfig.SpectralFrameScale;
// TODO: CONVERT IMAGE scales into Compression factors.
compressionCount = imageScales.Length;
compressionFactor = new int[compressionCount];
compressionFactor[compressionCount - 1] = 1;
double denom = imageScales[compressionCount - 1];
for (int i = 0; i < compressionCount - 1; i++)
{
compressionFactor[i] = (int)Math.Round(imageScales[i] / denom);
}
}
int maxCompression = compressionFactor[0];
TimeSpan maxImageDuration = TimeSpan.FromTicks(maxCompression * imageWidth * frameScale.Ticks);
TimeSpan halfMaxImageDuration = TimeSpan.FromMilliseconds(maxImageDuration.TotalMilliseconds / 2);
TimeSpan startTimeOfMaxImage = TimeSpan.Zero;
if (focalTime != TimeSpan.Zero)
{
startTimeOfMaxImage = focalTime - halfMaxImageDuration;
}
TimeSpan startTimeOfData = TimeSpan.FromMinutes(Math.Floor(startTimeOfMaxImage.TotalMinutes));
List <double[]> frameData = ReadFrameData(inputDirectory, fileStem, startTimeOfMaxImage, maxImageDuration, zoomConfig, indexGeneration.MaximumSegmentDuration.Value);
// get the index data to add into the
// TimeSpan imageScale1 = TimeSpan.FromSeconds(0.1);
double[,] indexData = spectra["POW"];
// make the images
for (int i = 0; i < compressionCount; i++)
{
int factor = compressionFactor[i];
var image = DrawFrameSpectrogramAtScale(ldsConfig, indexGeneration, startTimeOfData, factor, frameData, indexData, focalTime, frameScale, imageWidth);
if (image != null)
{
imageList.Add(image);
}
}
sw.Stop();
LoggedConsole.WriteLine("Finished spectrograms derived from standard frames. Elapsed time = " + sw.Elapsed.TotalSeconds + " seconds");
// combine the images into a stack
Image combinedImage = ImageTools.CombineImagesVertically(imageList);
string fileName = $"{fileStem}_FocalZOOM_min{focalTime.TotalMinutes:f1}.png";
combinedImage.Save(Path.Combine(outputDirectory.FullName, fileName));
}