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Rework rendering of Concatenated Indices
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Purpose of this was to get unit tests working. The most important work here was done in the gapsAndJoins class.
All unit tests for this class are now working.
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@towsey
towsey committed Mar 19, 2019
1 parent 668e48b commit d690c35
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Showing 5 changed files with 74 additions and 76 deletions.
119 changes: 60 additions & 59 deletions src/AudioAnalysisTools/Indices/GapsAndJoins.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -66,13 +66,13 @@ public class GapsAndJoins
/// <summary>
/// Does several data integrity checks.
/// </summary>
/// <param name="summaryIndices">a dictionary of summary indices</param>
/// <param name="gapRendering">describes how recording gaps are to be rendered</param>
/// <returns>a list of erroneous segments</returns>
/// <param name="summaryIndices">a dictionary of summary indices.</param>
/// <param name="gapRendering">describes how recording gaps are to be rendered.</param>
/// <returns>a list of erroneous segments.</returns>
public static List<GapsAndJoins> DataIntegrityCheck(IEnumerable<SummaryIndexValues> summaryIndices, ConcatMode gapRendering)
{
// Integrity check 1: look for whether a recording minute exists
var errors = DataIntegrityCheckForNoRecording(summaryIndices, gapRendering);
var errors = DataIntegrityCheckRecordingGaps(summaryIndices, gapRendering);

// Integrity check 2: look for whether there is join between two recording files
errors.AddRange(DataIntegrityCheckForFileJoins(summaryIndices, gapRendering));
Expand All @@ -88,21 +88,21 @@ public static List<GapsAndJoins> DataIntegrityCheck(IEnumerable<SummaryIndexValu
/// <summary>
/// Does three data integrity checks.
/// </summary>
/// <param name="spectralIndices">a dictionary of spectral indices</param>
/// <param name="gapRendering">how to render the gap in image terms</param>
/// <returns>a list of erroneous segments</returns>
/// <param name="spectralIndices">a dictionary of spectral indices.</param>
/// <param name="gapRendering">how to render the gap in image terms.</param>
/// <returns>a list of erroneous segments.</returns>
public static List<GapsAndJoins> DataIntegrityCheck(Dictionary<string, double[,]> spectralIndices, ConcatMode gapRendering)
{
var errors = DataIntegrityCheckSpectralIndices(spectralIndices, gapRendering);
return errors;
}

/// <summary>
/// Writes a list of erroneous segment properties to file
/// Writes a list of erroneous segment properties to file.
/// </summary>
/// <param name="errors">list of erroneous segments</param>
/// <param name="outputDirectory">directory in which json file to be written</param>
/// <param name="fileStem">name of json file</param>
/// <param name="errors">list of erroneous segments.</param>
/// <param name="outputDirectory">directory in which json file to be written.</param>
/// <param name="fileStem">name of json file.</param>
public static void WriteErrorsToFile(List<GapsAndJoins> errors, DirectoryInfo outputDirectory, string fileStem)
{
// write info to file
Expand All @@ -118,72 +118,79 @@ public static void WriteErrorsToFile(List<GapsAndJoins> errors, DirectoryInfo ou
}

/// <summary>
/// This method reads through a SUMMARY index array to make sure there was actually a signal to analyse.
/// If this occurs an gap/join event is flagged.
/// This method reads through a SUMMARY index array looking for gaps in the recording.
/// I initilly tried to detect these when the RankOrder index takes consecutive zero values.
/// However this does not work with recordings sampled one minute in N minutes.
/// So reverted to detecting the mising data flag which is when row.FileName == missingRow.
/// If this occurs a gap event is flagged.
/// </summary>
/// <param name="summaryIndices">array of summary indices</param>
/// <param name="gapRendering">how to render the gap in image terms</param>
/// <returns>a list of erroneous segments</returns>
public static List<GapsAndJoins> DataIntegrityCheckForNoRecording(IEnumerable<SummaryIndexValues> summaryIndices, ConcatMode gapRendering)
/// <param name="summaryIndices">array of summary indices.</param>
/// <param name="gapRendering">how to render the gap in image terms.</param>
/// <returns>a list of erroneous segments.</returns>
public static List<GapsAndJoins> DataIntegrityCheckRecordingGaps(IEnumerable<SummaryIndexValues> summaryIndices, ConcatMode gapRendering)
{
// init list of gaps and joins
var joins = new List<GapsAndJoins>();
string previousFileName = summaryIndices.First<SummaryIndexValues>().FileName;
var gaps = new List<GapsAndJoins>();

// now loop through the rows/vectors of indices
// initialise starting conditions for loop
string missingRow = IndexMatrices.MissingRowString;
//int previousRank = -1;
GapsAndJoins gap = null;
bool isGap = false;
int index = 0;

// now loop through the rows/vectors of indices
foreach (var row in summaryIndices)
{
//if (previousFileName == null)
//if (!isGap && (row.RankOrder == previousRank + 1))
//{
// previousFileName = row.FileName;
// //everything OK
// //continue;
//}

//if (row.FileName != previousFileName)
// if in gap and zeros continue then still in gap
//if (isGap && (row.RankOrder == 0 && previousRank == 0))
//{
// if (isValidBlock)
// {
// isValidBlock = false;
// fileJoin = new GapsAndJoins
// {
// StartPosition = index,
// GapDescription = gapDescriptionFileJoin,
// GapRendering = gapRendering,
// };
// }
// else
// {
// // come to end of a bad patch
// isValidBlock = true;
// fileJoin.EndPosition = index - 1;
// joins.Add(fileJoin);
// }
// //still in gap
// //continue;
//}

if (row.FileName != previousFileName)
//if (!isGap && (row.RankOrder == 0 && previousRank == 0))
if (!isGap && (row.FileName == missingRow))
{
var fileJoin = new GapsAndJoins
// create gap instance
isGap = true;
gap = new GapsAndJoins
{
StartPosition = index,
GapDescription = gapDescriptionFileJoin,
GapDescription = gapDescriptionMissingData,
GapRendering = gapRendering,
EndPosition = index, // this renders to one pixel width.
};
}

joins.Add(fileJoin);
previousFileName = row.FileName;
//if (isGap && (row.RankOrder == 1 && previousRank == 0))
if (isGap && (row.FileName != missingRow))
{
// come to end of a gap
isGap = false;
gap.EndPosition = index - 1;
gaps.Add(gap);
}

//previousRank = row.RankOrder;
index++;
}

// if not OK at end of the array, need to terminate the gap.
//if (!isValidBlock)
//{
// joins[joins.Count - 1].EndPosition = joins[joins.Count - 1].EndPosition;
//}
// reached end of array
// if still have gap at end of the array, need to terminate it.
if (isGap)
{
//gaps[gaps.Count - 1].EndPosition = index - 1;
gap.EndPosition = summaryIndices.Count() - 1;
gaps.Add(gap);
}

return joins;
return gaps;
}

/// <summary>
Expand Down Expand Up @@ -245,12 +252,6 @@ public static List<GapsAndJoins> DataIntegrityCheckForFileJoins(IEnumerable<Summ
index++;
}

// if not OK at end of the array, need to terminate the gap.
//if (!isValidBlock)
//{
// joins[joins.Count - 1].EndPosition = joins[joins.Count - 1].EndPosition;
//}

return joins;
}

Expand Down Expand Up @@ -447,7 +448,7 @@ public static List<GapsAndJoins> DataIntegrityCheckSpectralIndices(
}

/// <summary>
/// This method draws the error segments in in hierarchical order, highest level errors first.
/// This method draws the error segments in hierarchical order, highest level errors first.
/// This way error due to missing recording is drawn last and overwrites other casading errors due to missing recording.
/// </summary>
/// <param name="bmp">The chromeless spectrogram to have segments drawn on it.</param>
Expand Down
18 changes: 9 additions & 9 deletions src/AudioAnalysisTools/Indices/IndexDisplay.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ public static Bitmap DrawImageOfSummaryIndices(
continue;
}

string name = ip.Name;
//string name = ip.Name;
double[] array = dictionaryOfSummaryIndices[key];
scaleLength = array.Length;
Image bitmap = ip.GetPlotImage(array, errors);
Expand All @@ -144,25 +144,25 @@ public static Bitmap DrawImageOfSummaryIndices(
.Where(b => b != null).ToList();

//set up the composite image parameters
int X_offset = 2;
int graphWidth = X_offset + scaleLength;
int imageWidth = X_offset + scaleLength + TrackEndPanelWidth;
TimeSpan scaleDuration = TimeSpan.FromMinutes(scaleLength);
int imageHt = trackHeight * (listOfBitmaps.Count + 4); //+3 for title and top and bottom time tracks
int x_offset = 2;
int graphWidth = x_offset + scaleLength;
int imageWidth = x_offset + scaleLength + TrackEndPanelWidth;
//TimeSpan scaleDuration = TimeSpan.FromMinutes(scaleLength);
//int imageHt = trackHeight * (listOfBitmaps.Count + 4); //+3 for title and top and bottom time tracks
Bitmap titleBmp = ImageTrack.DrawTitleTrack(imageWidth, trackHeight, titleText);

//Bitmap time1Bmp = ImageTrack.DrawTimeTrack(scaleDuration, TimeSpan.Zero, DrawSummaryIndices.TimeScale, graphWidth, TrackHeight, "Time (hours)");
TimeSpan xAxisPixelDuration = indexCalculationDuration;
TimeSpan fullDuration = TimeSpan.FromTicks(xAxisPixelDuration.Ticks * graphWidth);
Bitmap timeBmp1 = ImageTrack.DrawTimeRelativeTrack(fullDuration, graphWidth, trackHeight);
Bitmap timeBmp2 = timeBmp1;
Bitmap suntrack = null;
//Bitmap suntrack = null;
DateTimeOffset? dateTimeOffset = recordingStartDate;
if (dateTimeOffset.HasValue)
{
// draw extra time scale with absolute start time. AND THEN Do SOMETHING WITH IT.
timeBmp2 = ImageTrack.DrawTimeTrack(fullDuration, dateTimeOffset, graphWidth, trackHeight);
suntrack = SunAndMoon.AddSunTrackToImage(scaleLength, dateTimeOffset, sunriseDataFile);
//suntrack = SunAndMoon.AddSunTrackToImage(scaleLength, dateTimeOffset, sunriseDataFile);
}

//draw the composite bitmap
Expand All @@ -175,7 +175,7 @@ public static Bitmap DrawImageOfSummaryIndices(
}

imageList.Add(timeBmp2);
imageList.Add(suntrack);
//imageList.Add(suntrack);
Bitmap compositeBmp = (Bitmap)ImageTools.CombineImagesVertically(imageList);
return compositeBmp;
}
Expand Down
4 changes: 2 additions & 2 deletions src/AudioAnalysisTools/Indices/IndexProperties.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -275,8 +275,8 @@ public Image GetPlotImage(double[] array, List<GapsAndJoins> errors = null)
int trackHeight = IndexDisplay.DefaultTrackHeight;
Color[] grayScale = ImageTools.GrayScale();

Bitmap bmp = new Bitmap(trackWidth, trackHeight);
Graphics g = Graphics.FromImage(bmp);
var bmp = new Bitmap(trackWidth, trackHeight);
var g = Graphics.FromImage(bmp);
g.Clear(grayScale[240]);

// for pixels in the line
Expand Down
7 changes: 2 additions & 5 deletions tests/Acoustics.Test/AnalysisPrograms/Concatenation/ConcatenationTests.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,13 @@ namespace Acoustics.Test.AnalysisPrograms.Concatenation
using System.IO;
using System.IO.Compression;
using System.Linq;

using Acoustics.Shared;
using global::AnalysisPrograms;

using global::AudioAnalysisTools.Indices;
using global::AudioAnalysisTools.LongDurationSpectrograms;
using global::TowseyLibrary;
using Microsoft.VisualStudio.TestTools.UnitTesting;
using TestHelpers;
using TowseyLibrary;

/// <summary>
/// Test methods for the various Frequency Scales
Expand Down Expand Up @@ -341,7 +338,7 @@ public void SampledDataConcatModeTests(ConcatMode gapRendering, int[] expectedWi
var actualImage = ImageTools.ReadImage2Bitmap(imagePath);
Assert.That.ImageIsSize(expectedWidth, 632, actualImage);

// target region for each image: 40,254, 20,20
// target region for each image: 40, 254, 20,20
switch (gapRendering)
{
case ConcatMode.TimedGaps:
Expand All @@ -355,7 +352,7 @@ public void SampledDataConcatModeTests(ConcatMode gapRendering, int[] expectedWi
case ConcatMode.NoGaps:
// There should basically be no pattern here
var histogram = ImageTools.GetColorHistogramNormalized(
actualImage,
actualImage,
new Rectangle(40, 254, 20, 20));

// should not have empty space
Expand Down
2 changes: 1 addition & 1 deletion tests/Acoustics.Test/InfiniteTextStreamTests.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ void Generate()
}
}

var work = Task.Run(Generate, token);
var work = Task.Run((Action)Generate, token);

Assert.IsFalse(work.IsCompleted);
source.CancelAfter(this.timeout);
Expand Down

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