public void TestMsFeatureScatterPlot(string path1, string path2, string pngPath) { // Convert relative paths to absolute paths path1 = GetPath(path1); path2 = GetPath(path2); pngPath = GetPath(pngPath); var fiOutput = new FileInfo(pngPath); var didirectory = fiOutput.Directory; if (didirectory == null) { throw new DirectoryNotFoundException(pngPath); } if (!didirectory.Exists) { didirectory.Create(); } var aligner = new LcmsWarpFeatureAligner(new LcmsWarpAlignmentOptions()); var isosFilterOptions = new DeconToolsIsosFilterOptions(); var baselineMs = UmcLoaderFactory.LoadMsFeatureData(path1, isosFilterOptions); var aligneeMs = UmcLoaderFactory.LoadMsFeatureData(path2, isosFilterOptions); var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased); var tolerances = new FeatureTolerances { FragmentationWindowSize = .5, Mass = 13, DriftTime = .3, Net = .01 }; var options = new LcmsFeatureFindingOptions(tolerances); options.MaximumNetRange = .002; var baseline = finder.FindFeatures(baselineMs, options, null); var alignee = finder.FindFeatures(aligneeMs, options, null); var alignmentResults = aligner.Align(baseline, alignee); var plotModel1 = new PlotModel { Subtitle = "Interpolated, cartesian axes", Title = "HeatMapSeries" }; var palette = OxyPalettes.Hot(200); var linearColorAxis1 = new LinearColorAxis { InvalidNumberColor = OxyColors.Gray, Position = AxisPosition.Right, Palette = palette }; plotModel1.Axes.Add(linearColorAxis1); // linearColorAxis1. var linearAxis1 = new LinearAxis { Position = AxisPosition.Bottom }; plotModel1.Axes.Add(linearAxis1); var linearAxis2 = new LinearAxis(); plotModel1.Axes.Add(linearAxis2); var heatMapSeries1 = new HeatMapSeries { X0 = 0, X1 = 1, Y0 = 0, Y1 = 1, FontSize = .2 }; var scores = alignmentResults.HeatScores; var width = scores.GetLength(0); var height = scores.GetLength(1); heatMapSeries1.Data = new double[width, height]; var seriesData = heatMapSeries1.Data; for (var i = 0; i < width; i++) { for (var j = 0; j < height; j++) { seriesData[i, j] = Convert.ToDouble(scores[i, j]); } } plotModel1.Series.Add(heatMapSeries1); var svg = new SvgExporter(); var svgString = svg.ExportToString(plotModel1); var xml = new XmlDocument(); xml.LoadXml(svgString); var x = SvgDocument.Open(xml); // Svg.SvgDocument(); var bmp = x.Draw(); bmp.Save(pngPath); var heatmap = HeatmapFactory.CreateAlignedHeatmap(alignmentResults.HeatScores, false); var netHistogram = HistogramFactory.CreateHistogram(alignmentResults.NetErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(alignmentResults.MassErrorHistogram, "Mass Error", "Mass Error (ppm)"); var baseName = Path.Combine(didirectory.FullName, Path.GetFileNameWithoutExtension(fiOutput.Name)); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, baseName + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netHistogram, baseName + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, baseName + "_massHistogram.svg", encoder); }
public void TestMsFeatureScatterPlot(string path1, string path2, string pngPath) { // Convert relative paths to absolute paths path1 = GetPath(path1); path2 = GetPath(path2); pngPath = GetPath(pngPath); var fiOutput = new FileInfo(pngPath); var didirectory = fiOutput.Directory; if (didirectory == null) throw new DirectoryNotFoundException(pngPath); if (!didirectory.Exists) didirectory.Create(); var aligner = new LcmsWarpFeatureAligner(); var baselineMs = UmcLoaderFactory.LoadMsFeatureData(path1); var aligneeMs = UmcLoaderFactory.LoadMsFeatureData(path2); var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased); var tolerances = new FeatureTolerances { FragmentationWindowSize = .5, Mass = 13, DriftTime = .3, Net = .01 }; var options = new LcmsFeatureFindingOptions(tolerances); options.MaximumNetRange = .002; var baseline = finder.FindFeatures(baselineMs, options, null); var alignee = finder.FindFeatures(aligneeMs, options, null); var alignmentResults = aligner.Align(baseline, alignee); var plotModel1 = new PlotModel { Subtitle = "Interpolated, cartesian axes", Title = "HeatMapSeries" }; var palette = OxyPalettes.Hot(200); var linearColorAxis1 = new LinearColorAxis { InvalidNumberColor = OxyColors.Gray, Position = AxisPosition.Right, Palette = palette }; plotModel1.Axes.Add(linearColorAxis1); // linearColorAxis1. var linearAxis1 = new LinearAxis {Position = AxisPosition.Bottom}; plotModel1.Axes.Add(linearAxis1); var linearAxis2 = new LinearAxis(); plotModel1.Axes.Add(linearAxis2); var heatMapSeries1 = new HeatMapSeries { X0 = 0, X1 = 1, Y0 = 0, Y1 = 1, FontSize = .2 }; var scores = alignmentResults.heatScores; var width = scores.GetLength(0); var height = scores.GetLength(1); heatMapSeries1.Data = new double[width, height]; var seriesData = heatMapSeries1.Data; for (var i = 0; i < width; i++) { for (var j = 0; j < height; j++) { seriesData[i, j] = Convert.ToDouble(scores[i, j]); } } plotModel1.Series.Add(heatMapSeries1); var svg = new SvgExporter(); var svgString = svg.ExportToString(plotModel1); var xml = new XmlDocument(); xml.LoadXml(svgString); var x = SvgDocument.Open(xml); // Svg.SvgDocument(); var bmp = x.Draw(); bmp.Save(pngPath); var heatmap = HeatmapFactory.CreateAlignedHeatmap(alignmentResults.heatScores); var netHistogram = HistogramFactory.CreateHistogram(alignmentResults.netErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(alignmentResults.massErrorHistogram, "Mass Error", "Mass Error (ppm)"); var baseName = Path.Combine(didirectory.FullName, Path.GetFileNameWithoutExtension(fiOutput.Name)); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, baseName + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netHistogram, baseName + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, baseName + "_massHistogram.svg", encoder); }
public void TestLcmsWarpPortCpp(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name) { var baselinePath = GetPath(relativeBaselinePath); var aligneePath = GetPath(relativeAligneePath); var aligner = new LcmsWarpFeatureAligner(); var rawBaselineData = File.ReadAllLines(baselinePath); var rawFeaturesData = File.ReadAllLines(aligneePath); var outputPath = GetOutputPath(relativeOutput); var delimiter = new[] {TextDelimiter}; if (!Directory.Exists(outputPath)) { Directory.CreateDirectory(outputPath); } var baseline = (from line in rawBaselineData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var features = (from line in rawFeaturesData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var maxd = features.Max(x => x.Net); var mind = features.Min(x => x.Net); if (maxd - mind < double.Epsilon) throw new Exception("There is something wrong with the features NET values"); aligner.Options.AlignType = AlignmentType.NET_MASS_WARP; var outputData = aligner.Align(baseline, features); var residuals = outputData.ResidualData; var heatmap = HeatmapFactory.CreateAlignedHeatmap(outputData.heatScores); var netHistogram = HistogramFactory.CreateHistogram(outputData.netErrorHistogram, "NET Error Histogram", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(outputData.massErrorHistogram, "Mass Error Histogram", "Mass Error (ppm)"); var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Scan, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); var massMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); var massScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Scan, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); var directory = Path.Combine(outputPath, name); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.svg", encoder); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.svg", encoder); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.svg", encoder); PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.svg", encoder); }
/// <summary> /// Shows the encoder settings dialog and initializes the encoder. /// </summary> /// <param name="encoder">The encoder.</param> /// <param name="canAddImagesToExistingFile">The value indicating whether encoder can add images to the existing multipage image file.</param> /// <returns> /// <b>True</b> if settings are applied to the encoder; otherwise, <b>false</b>. /// </returns> protected virtual bool ShowEncoderSettingsDialog( ref EncoderBase encoder, bool canAddImagesToExistingFile) { // set encoder settings switch (encoder.Name) { case "Bmp": using (BmpEncoderSettingsForm bmpEncoderSettingsForm = new BmpEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(bmpEncoderSettingsForm); if (bmpEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } BmpEncoder bmpEncoder = (BmpEncoder)encoder; bmpEncoder.Settings = bmpEncoderSettingsForm.EncoderSettings; return(true); } case "Png": using (PngEncoderSettingsForm pngEncoderSettingsForm = new PngEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(pngEncoderSettingsForm); if (pngEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } PngEncoder pngEncoder = (PngEncoder)encoder; pngEncoder.Settings = pngEncoderSettingsForm.EncoderSettings; return(true); } case "Gif": using (GifEncoderSettingsForm gifEncoderSettingsForm = new GifEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(gifEncoderSettingsForm); gifEncoderSettingsForm.CanAddImagesToExistingFile = canAddImagesToExistingFile; if (gifEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } GifEncoder gifEncoder = (GifEncoder)encoder; gifEncoder.Settings = gifEncoderSettingsForm.EncoderSettings; gifEncoder.CreateNewFile = !gifEncoderSettingsForm.AddImagesToExistingFile; return(true); } case "Jpeg": using (JpegEncoderSettingsForm jpegEncoderSettingsForm = new JpegEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(jpegEncoderSettingsForm); if (jpegEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } JpegEncoder jpegEncoder = (JpegEncoder)encoder; jpegEncoder.Settings = jpegEncoderSettingsForm.EncoderSettings; return(true); } case "Tiff": using (TiffEncoderSettingsForm tiffEncoderSettingsForm = new TiffEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(tiffEncoderSettingsForm); tiffEncoderSettingsForm.CanAddImagesToExistingFile = canAddImagesToExistingFile; if (tiffEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } TiffEncoder tiffEncoder = (TiffEncoder)encoder; tiffEncoder.Settings = tiffEncoderSettingsForm.EncoderSettings; tiffEncoder.CreateNewFile = !tiffEncoderSettingsForm.AddImagesToExistingFile; return(true); } case "Svg": using (SvgEncoderSettingsForm svgEncoderSettingsForm = new SvgEncoderSettingsForm()) { SetEncoderSettingsDialogProperties(svgEncoderSettingsForm); if (svgEncoderSettingsForm.ShowDialog() != DialogResult.OK) { return(false); } SvgEncoder svgEncoder = (SvgEncoder)encoder; svgEncoder.Settings = svgEncoderSettingsForm.EncoderSettings; return(true); } } return(false); }
private static void TestNow(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name) { string baselinePath = GetPath(relativeBaselinePath); var aligneePath = GetPath(relativeAligneePath); var aligner = new LcmsWarpFeatureAligner(); var rawBaselineData = File.ReadAllLines(baselinePath); var rawFeaturesData = File.ReadAllLines(aligneePath); var outputPath = GetOutputPath(relativeOutput); var delimiter = new[] { TextDelimiter }; if (!Directory.Exists(outputPath)) { Directory.CreateDirectory(outputPath); } var baseline = (from line in rawBaselineData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var features = (from line in rawFeaturesData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var maxd = features.Max(x => x.Net); var mind = features.Min(x => x.Net); if (maxd - mind < double.Epsilon) { throw new Exception("There is something wrong with the features NET values"); } aligner.Options.AlignType = AlignmentType.NET_MASS_WARP; var outputData = aligner.Align(baseline, features); var residuals = outputData.ResidualData; using (var writer = new StreamWriter(@"E:\MultiAlignTest\Results\heat-scores-old.txt")) { foreach (var oovarscore in outputData.heatScores) { writer.WriteLine(oovarscore); } } var heatmap = HeatmapFactory.CreateAlignedHeatmap(outputData.heatScores); var netHistogram = HistogramFactory.CreateHistogram(outputData.netErrorHistogram, "NET Error Histogram", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(outputData.massErrorHistogram, "Mass Error Histogram", "Mass Error (ppm)"); var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Scan, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); var massMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); var massScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Scan, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); var directory = Path.Combine(outputPath, name); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.svg", encoder); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.svg", encoder); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.svg", encoder); //PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.svg", encoder); }
public void TestLcmsWarpPort(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name) { var baselinePath = GetPath(relativeBaselinePath); var aligneePath = GetPath(relativeAligneePath); var options = new LcmsWarpAlignmentOptions { AlignType = LcmsWarpAlignmentType.NET_MASS_WARP, CalibrationType = LcmsWarpCalibrationType.Both }; var aligner = new LcmsWarpFeatureAligner(options); var rawBaselineData = File.ReadAllLines(baselinePath); var rawFeaturesData = File.ReadAllLines(aligneePath); var outputPath = GetOutputPath(relativeOutput); var delimiter = new[] { TextDelimiter }; if (!Directory.Exists(outputPath)) { Directory.CreateDirectory(outputPath); } var baseline = (from line in rawBaselineData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var features = (from line in rawFeaturesData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var outputData = aligner.Align(baseline, features); var residuals = outputData.ResidualData; var heatmap = HeatmapFactory.CreateAlignedHeatmap(outputData.HeatScores, false); var netHistogram = HistogramFactory.CreateHistogram(outputData.NetErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(outputData.MassErrorHistogram, "Mass Error", "Mass Error (ppm)"); var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); var massMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); var massScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); var directory = Path.Combine(outputPath, name); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.svg", encoder); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.svg", encoder); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.svg", encoder); PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.svg", encoder); }