Skip to content

Commit

Permalink
Creates and fixes unit tests for ConcatModes
Browse files Browse the repository at this point in the history 
This patch completed unit testing for the ConcatModes code from #138 and #136.

It also adds in a bunch of new handy image assertions! 🆒

It also changes the way the GapAndJoins class works - it now takes a strongly typed SummaryIndexValues wich allows for less hacky (and faster!) code. Additionally, the two properties added to SummaryIndexValues in 64ac921 were removed and calculations for gaps/missing files were altered to use fields that were already in the class!!! This will potentially save GBs of wasted space because the SummaryIndexValues class was outputting blank columns when doing index generation.
  • Loading branch information
@atruskie
atruskie committed Dec 18, 2017
1 parent bf877a8 commit 29d178b
Show file tree
Hide file tree
Showing 11 changed files with 412 additions and 241 deletions.
1 change: 0 additions & 1 deletion Acoustics/Acoustics.Shared/Csv/Csv.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,6 @@ public static void WriteToCsv<T>(FileInfo destination, IEnumerable<T> results)
/// Read an object from a CSV file.
/// </summary>
/// <remarks>
/// This has not been tested yet! Contact anthony if you have problems.
/// IMPORTANT NOTE:
/// If I get an exception, how do I tell what line the exception is on?
/// There is a lot of information held in Exception.Data["CsvHelper"]
Expand Down
7 changes: 7 additions & 0 deletions Acoustics/Acoustics.Shared/Extensions/RandomExtensions.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
namespace Acoustics.Shared.Extensions
{
using System;
using System.Drawing;
using System.Collections.Generic;
using System.Linq;
using System.Text;
Expand Down Expand Up @@ -93,5 +94,11 @@ public static Range<double> NextRange(this Random random, double min = 0, double
return new Range<double>(b, a);
}
}

public static Color NextColor(this Random random, byte alpha = 255)
{
var value = random.Next();
return Color.FromArgb(alpha, Color.FromArgb(value));
}
}
}
8 changes: 7 additions & 1 deletion Acoustics/Acoustics.Shared/Extensions/RectangleExtensions.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@
// All code in this file and all associated files are the copyright and property of the QUT Ecoacoustics Research Group (formerly MQUTeR, and formerly QUT Bioacoustics Research Group).
// </copyright>

namespace Acoustics.Shared.Extensions
// ReSharper disable once CheckNamespace
namespace System.Drawing
{
using System;
using System.Collections.Generic;
Expand All @@ -12,6 +13,11 @@ namespace Acoustics.Shared.Extensions

public static class RectangleExtensions
{
public static int Area(this Rectangle rectangle)
{
return rectangle.Width * rectangle.Height;
}

public static bool PointIntersect(this Rectangle rectangle, Point point)
{
return point.X >= rectangle.Left && point.X < rectangle.Right && point.Y >= rectangle.Bottom
Expand Down
151 changes: 89 additions & 62 deletions Acoustics/Acoustics.Test/AnalysisPrograms/Concatenation/ConcatenationTests.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,12 @@ namespace Acoustics.Test.AnalysisPrograms.Concatenation
using System.Drawing;
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;
Expand Down Expand Up @@ -51,17 +54,6 @@ public static void MyClassInitialize(TestContext testContext)
ZipFile.ExtractToDirectory(newZealandIndices.FullName, newZealandArk01IndicesDirectory.FullName);
}

/*
* An example of modifying a default config file
// get the default config file
var defaultConfigFile = PathHelper.ResolveConfigFile("SpectrogramFalseColourConfig.yml");
var config = Yaml.Deserialise<LdSpectrogramConfig>(defaultConfigFile);
// make changes to config file as required for test
var testConfig = new FileInfo(this.outputDirectory + "\\SpectrogramFalseColourConfig.yml");
Yaml.Serialise(testConfig, config);
*/

/// <summary>
/// METHOD TO CHECK Concatenation of spectral and summary index files when
/// ConcatenateEverythingYouCanLayYourHandsOn = true
Expand All @@ -70,7 +62,6 @@ public static void MyClassInitialize(TestContext testContext)
public void ConcatenateEverythingYouCanLayYourHandsOn()
{
// top level directory
DirectoryInfo[] dataDirs = { indonesiaIndicesDirectory };
var indexPropertiesConfig = PathHelper.ResolveConfigFile("IndexPropertiesConfig.yml");
var dateString = "20160725";

Expand All @@ -79,7 +70,7 @@ public void ConcatenateEverythingYouCanLayYourHandsOn()

var arguments = new ConcatenateIndexFiles.Arguments
{
InputDataDirectories = dataDirs,
InputDataDirectories = new[] { indonesiaIndicesDirectory },
OutputDirectory = this.outputDirectory,
DirectoryFilter = "*.wav",
FileStemName = "Test1_Indonesia",
Expand Down Expand Up @@ -112,10 +103,10 @@ public void ConcatenateEverythingYouCanLayYourHandsOn()
Assert.That.FileNotExists(outputDataDir.CombineFile(prefix + "SummaryIndex.csv"));

var actualImage = ImageTools.ReadImage2Bitmap(imageFileInfo.FullName);
ImageAssert.IsSize(722, 632, actualImage);
ImageAssert.PixelIsColor(new Point(100, 100), Color.FromArgb(211, 211, 211), actualImage);
ImageAssert.PixelIsColor(new Point(200, 100), Color.FromArgb(54, 29, 18), actualImage);
ImageAssert.PixelIsColor(new Point(675, 600), Color.FromArgb(255, 105, 180), actualImage);
Assert.That.ImageIsSize(722, 632, actualImage);
Assert.That.PixelIsColor(new Point(100, 100), Color.FromArgb(211, 211, 211), actualImage);
Assert.That.PixelIsColor(new Point(200, 100), Color.FromArgb(54, 29, 18), actualImage);
Assert.That.PixelIsColor(new Point(675, 600), Color.FromArgb(255, 105, 180), actualImage);
}

/// <summary>
Expand All @@ -126,7 +117,6 @@ public void ConcatenateEverythingYouCanLayYourHandsOn()
public void ConcatenateIndexFilesTest24Hour()
{
// top level directory
DirectoryInfo[] dataDirs = { indonesiaIndicesDirectory };
var indexPropertiesConfig = PathHelper.ResolveConfigFile("IndexPropertiesConfig.yml");
var dateString = "20160726";

Expand All @@ -135,7 +125,7 @@ public void ConcatenateIndexFilesTest24Hour()

var arguments = new ConcatenateIndexFiles.Arguments
{
InputDataDirectories = dataDirs,
InputDataDirectories = new[] { indonesiaIndicesDirectory },
OutputDirectory = this.outputDirectory,
DirectoryFilter = "*.wav",
FileStemName = "Test2_Indonesia",
Expand Down Expand Up @@ -170,9 +160,9 @@ public void ConcatenateIndexFilesTest24Hour()

var actualImage = ImageTools.ReadImage2Bitmap(imageFileInfo.FullName);
// we expect only the second half (past midnight) of the image to be rendered
ImageAssert.IsSize(512, 632, actualImage);
ImageAssert.PixelIsColor(new Point(100, 100), Color.FromArgb(32, 25, 36), actualImage);
ImageAssert.PixelIsColor(new Point(100, 160), Color.FromArgb(0, 80, 132), actualImage);
Assert.That.ImageIsSize(512, 632, actualImage);
Assert.That.PixelIsColor(new Point(100, 100), Color.FromArgb(32, 25, 36), actualImage);
Assert.That.PixelIsColor(new Point(100, 160), Color.FromArgb(0, 80, 132), actualImage);
}

/// <summary>
Expand All @@ -185,16 +175,14 @@ public void ConcatenateIndexFilesTest24Hour()
[TestMethod]
public void ConcatenateIndexFilesTest24HourWithoutDateRange()
{
// top level directory
DirectoryInfo[] dataDirs = { indonesiaIndicesDirectory };
var indexPropertiesConfig = PathHelper.ResolveConfigFile("IndexPropertiesConfig.yml");

// get the default config file
var testConfig = PathHelper.ResolveConfigFile("SpectrogramFalseColourConfig.yml");

var arguments = new ConcatenateIndexFiles.Arguments
{
InputDataDirectories = dataDirs,
InputDataDirectories = new[] { indonesiaIndicesDirectory },
OutputDirectory = this.outputDirectory,
DirectoryFilter = "*.wav",
FileStemName = "Test3_Indonesia",
Expand Down Expand Up @@ -228,9 +216,9 @@ public void ConcatenateIndexFilesTest24HourWithoutDateRange()
Assert.That.FileNotExists(outputDataDir1.CombineFile(prefix1 + "SummaryIndex.csv"));

var actualImage1 = ImageTools.ReadImage2Bitmap(image1FileInfo.FullName);
ImageAssert.IsSize(210, 632, actualImage1);
ImageAssert.PixelIsColor(new Point(100, 100), Color.FromArgb(211, 211, 211), actualImage1);
ImageAssert.PixelIsColor(new Point(50, 50), Color.FromArgb(86, 29, 17), actualImage1);
Assert.That.ImageIsSize(210, 632, actualImage1);
Assert.That.PixelIsColor(new Point(100, 100), Color.FromArgb(211, 211, 211), actualImage1);
Assert.That.PixelIsColor(new Point(50, 50), Color.FromArgb(86, 29, 17), actualImage1);

// IMAGE 2: Compare image files - check that image exists and dimensions are correct
var dateString2 = "20160726";
Expand All @@ -244,9 +232,9 @@ public void ConcatenateIndexFilesTest24HourWithoutDateRange()
Assert.That.FileNotExists(outputDataDir2.CombineFile(prefix2 + "SummaryIndex.csv"));

var actualImage2 = ImageTools.ReadImage2Bitmap(image2FileInfo.FullName);
ImageAssert.IsSize(512, 632, actualImage2);
ImageAssert.PixelIsColor(new Point(50, 124), Color.FromArgb(70, 38, 255), actualImage2);
ImageAssert.PixelIsColor(new Point(460, 600), Color.FromArgb(255, 105, 180), actualImage2);
Assert.That.ImageIsSize(512, 632, actualImage2);
Assert.That.PixelIsColor(new Point(50, 124), Color.FromArgb(70, 38, 255), actualImage2);
Assert.That.PixelIsColor(new Point(460, 600), Color.FromArgb(255, 105, 180), actualImage2);
}

/// <summary>
Expand All @@ -255,8 +243,6 @@ public void ConcatenateIndexFilesTest24HourWithoutDateRange()
[TestMethod]
public void ConcatenateIndexFilesTestConfigFileChanges()
{
// top level directory
DirectoryInfo[] dataDirs = { indonesiaIndicesDirectory };
var indexPropertiesConfig = PathHelper.ResolveConfigFile("IndexPropertiesConfig.yml");
var dateString = "20160726";

Expand All @@ -274,7 +260,7 @@ public void ConcatenateIndexFilesTestConfigFileChanges()

var arguments = new ConcatenateIndexFiles.Arguments
{
InputDataDirectories = dataDirs,
InputDataDirectories = new[] { indonesiaIndicesDirectory },
OutputDirectory = this.outputDirectory,
DirectoryFilter = "*.wav",
FileStemName = "Test2_Indonesia",
Expand Down Expand Up @@ -307,55 +293,96 @@ public void ConcatenateIndexFilesTestConfigFileChanges()
Assert.IsTrue(imageFileInfo2.Exists);
}

[TestMethod]
public void ConcatenateIndexFilesSampledDataGapsTest()
/// <summary>
/// These tests use a dataset constructed from one-minute long samples, recorded every 20-min.
/// Thus there's a column of data for every 20 pixels.
/// </summary>
[DataTestMethod]
[DataRow(ConcatMode.TimedGaps, new [] {1440, 1420, 1440})]
[DataRow(ConcatMode.NoGaps, new[] { 73, 72, 73 })]
[DataRow(ConcatMode.EchoGaps, new[] { 1440, 1420, 1440 })]
public void SampledDataConcatModeTests(ConcatMode gapRendering, int[] expectedWidths)
{
const string Ark01 = "Ark01";

var arguments = new ConcatenateIndexFiles.Arguments
{
InputDataDirectories = new DirectoryInfo[] { newZealandArk01IndicesDirectory },
InputDataDirectories = new[] { newZealandArk01IndicesDirectory },
OutputDirectory = this.outputDirectory,
DirectoryFilter = "*.wav",
FileStemName = "Test3_Indonesia",
FileStemName = Ark01,
StartDate = null,
EndDate = null,
IndexPropertiesConfig = PathHelper.ResolveConfigFile("IndexPropertiesConfig.yml"),
FalseColourSpectrogramConfig = PathHelper.ResolveConfigFile("SpectrogramFalseColourConfig.yml"),
ColorMap1 = null,
ColorMap2 = null,
ConcatenateEverythingYouCanLayYourHandsOn = false, // 24 hour blocks only
ConcatenateEverythingYouCanLayYourHandsOn = false,
GapRendering = gapRendering,
TimeSpanOffsetHint = TimeSpan.FromHours(12),
DrawImages = true,
};

ConcatenateIndexFiles.Execute(arguments);

// There should be three sets of output images one for each partial day.
// TODO: finish new zealand tests for all 3 modes - TimeGaps, No Gaps, EchoGaps
Assert.Fail("Not yet completed");
var dateStrings = new[] {"20161209", "20161210", "20161211"}.Zip(expectedWidths, ValueTuple.Create);
foreach (var (dateString, expectedWidth) in dateStrings)
{
var prefix = Path.Combine(this.outputDirectory.FullName, Ark01, dateString, Ark01 + "_" + dateString + "__");

// IMAGE 1: Compare image files - check that image exists and dimensions are correct
var dateString1 = "20160725";
var outputDataDir1 = this.outputDirectory.Combine(arguments.FileStemName, dateString1);
string image1FileName = arguments.FileStemName + "_" + dateString1 + "__2Maps.png";
var image1FileInfo = outputDataDir1.CombineFile(outputDataDir1.FullName, image1FileName);
Assert.IsTrue(image1FileInfo.Exists);
Assert.That.PathExists(prefix + "Towsey.Acoustic.Indices.csv");
Assert.That.PathNotExists(prefix + "SummaryIndex.csv");

var actualImage1 = ImageTools.ReadImage2Bitmap(image1FileInfo.FullName);
ImageAssert.IsSize(210, 632, actualImage1);
ImageAssert.PixelIsColor(new Point(100, 100), Color.FromArgb(211, 211, 211), actualImage1);
ImageAssert.PixelIsColor(new Point(50, 50), Color.FromArgb(86, 29, 17), actualImage1);
var imagePath = prefix + "2Maps.png";
Assert.That.FileExists(imagePath);

// IMAGE 2: Compare image files - check that image exists and dimensions are correct
var dateString2 = "20160726";
var outputDataDir2 = this.outputDirectory.Combine(arguments.FileStemName, dateString2);
string image2FileName = arguments.FileStemName + "_" + dateString2 + "__2Maps.png";
var image2FileInfo = outputDataDir2.CombineFile(image2FileName);
Assert.IsTrue(image2FileInfo.Exists);
var actualImage = ImageTools.ReadImage2Bitmap(imagePath);
Assert.That.ImageIsSize(expectedWidth, 632, actualImage);

var actualImage2 = ImageTools.ReadImage2Bitmap(image2FileInfo.FullName);
ImageAssert.IsSize(512, 632, actualImage2);
ImageAssert.PixelIsColor(new Point(50, 124), Color.FromArgb(70, 38, 255), actualImage2);
ImageAssert.PixelIsColor(new Point(460, 600), Color.FromArgb(255, 105, 180), actualImage2);
// target region for each image: 40,254, 20,20
switch (gapRendering)
{
case ConcatMode.TimedGaps:
// for timed gap, first column has content, other 19 don't and should be gray (missing data)
Assert.That.ImageRegionIsColor(
new Rectangle(40 + 1, 254, 20 - 1, 20),
Color.LightGray,
actualImage,
0.001);
break;
case ConcatMode.NoGaps:
// There should basically be no pattern here
var histogram = ImageTools.GetColorHistogramNormalized(
actualImage,
new Rectangle(40, 254, 20, 20));

// should not have empty space
var hasGray = histogram.TryGetValue(Color.LightGray, out var grayPercentage);
Assert.IsTrue(!hasGray || grayPercentage < 0.01);

// the rest of the values should be well distributed (not a perfect test)
Assert.That.ImageColorsWellDistributed(
actualImage,
allowedError: 0.1,
colorHistogram: histogram);

break;
case ConcatMode.EchoGaps:
// The first column should be repeated 19 times
Assert.That.ImageRegionIsRepeatedHorizontally(
new Rectangle(40, 254, 1, 20),
19,
1,
actualImage,
0.0);
break;
default:
throw new ArgumentOutOfRangeException(nameof(gapRendering), gapRendering, null);
}

}
}


}
}
4 changes: 2 additions & 2 deletions Acoustics/Acoustics.Test/Shared/CsvTests.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -351,8 +351,8 @@ public void TestBaseTypesAreNotSerializedAsArray()
var baseExpected = $@"{nameof(SummaryIndexBase.RankOrder)},{nameof(SummaryIndexBase.FileName)},{nameof(SummaryIndexBase.ResultStartSeconds)},{nameof(SummaryIndexBase.SegmentDurationSeconds)},{nameof(SummaryIndexBase.ResultMinute)}
0,,0,0,0
".NormalizeToCrLf();
var childExpected = $@"NoFile,ZeroSignal,HighAmplitudeIndex,ClippingIndex,AvgSignalAmplitude,BackgroundNoise,Snr,AvgSnrOfActiveFrames,Activity,EventsPerSecond,HighFreqCover,MidFreqCover,LowFreqCover,AcousticComplexity,TemporalEntropy,EntropyOfAverageSpectrum,AvgEntropySpectrum,EntropyOfVarianceSpectrum,VarianceEntropySpectrum,EntropyOfPeaksSpectrum,EntropyPeaks,EntropyOfCoVSpectrum,ClusterCount,ThreeGramCount,Ndsi,SptDensity,{nameof(SummaryIndexBase.RankOrder)},{nameof(SummaryIndexBase.FileName)},{nameof(SummaryIndexBase.ResultStartSeconds)},{nameof(SummaryIndexBase.SegmentDurationSeconds)},{nameof(SummaryIndexBase.ResultMinute)}
0,0,0,0,-100,-100,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,0,0,0
var childExpected = $@"ZeroSignal,HighAmplitudeIndex,ClippingIndex,AvgSignalAmplitude,BackgroundNoise,Snr,AvgSnrOfActiveFrames,Activity,EventsPerSecond,HighFreqCover,MidFreqCover,LowFreqCover,AcousticComplexity,TemporalEntropy,EntropyOfAverageSpectrum,AvgEntropySpectrum,EntropyOfVarianceSpectrum,VarianceEntropySpectrum,EntropyOfPeaksSpectrum,EntropyPeaks,EntropyOfCoVSpectrum,ClusterCount,ThreeGramCount,Ndsi,SptDensity,{nameof(SummaryIndexBase.RankOrder)},{nameof(SummaryIndexBase.FileName)},{nameof(SummaryIndexBase.ResultStartSeconds)},{nameof(SummaryIndexBase.SegmentDurationSeconds)},{nameof(SummaryIndexBase.ResultMinute)}
0,0,0,-100,-100,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,0,0,0
".NormalizeToCrLf();

Csv.WriteToCsv(this.testFile, childArray);
Expand Down
Loading

0 comments on commit 29d178b

Please sign in to comment.