public ChromGraphItem(TransitionGroupDocNode transitionGroupNode, TransitionDocNode transition, ChromatogramInfo chromatogram, TransitionChromInfo tranPeakInfo, IRegressionFunction timeRegressionFunction, bool[] annotatePeaks, double[] dotProducts, double bestProduct, bool isFullScanMs, bool isSummary, RawTimesInfoItem?displayRawTimes, int step, Color color, float fontSize, int width, FullScanInfo fullScanInfo = null) { TransitionGroupNode = transitionGroupNode; TransitionNode = transition; Chromatogram = chromatogram; TransitionChromInfo = tranPeakInfo; TimeRegressionFunction = timeRegressionFunction; Color = color; FullScanInfo = fullScanInfo; _step = step; _fontSpec = CreateFontSpec(color, fontSize); _width = width; _dotProducts = dotProducts; _bestProduct = bestProduct; _isFullScanMs = isFullScanMs; _isSummary = isSummary; _displayRawTimes = displayRawTimes; _arrayLabelIndexes = new int[annotatePeaks.Length]; if (chromatogram == null) { _measuredTimes = new double[0]; _displayTimes = _measuredTimes; _intensities = new double[0]; } else { // Cache values early to avoid accessing slow enumerators // which show up under profiling. Chromatogram.AsArrays(out _measuredTimes, out _intensities); if (TimeRegressionFunction == null) { _displayTimes = _measuredTimes; } else { _displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray(); } // Add peak times to hash set for labeling int iLastStart = 0; for (int i = 0; i < chromatogram.NumPeaks; i++) { int maxIndex = -1; if (annotatePeaks[i]) { ChromPeak peak = chromatogram.GetPeak(i); maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart); } _arrayLabelIndexes[i] = maxIndex; if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex)) { _annotatedTimes.Add(maxIndex, i); } } // Calculate best peak index if (tranPeakInfo != null) { iLastStart = 0; _bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart); } } }
private void ShadeGraph(TransitionChromInfo tranPeakInfo, ChromatogramInfo info, IRegressionFunction timeRegressionFunction, double[] dotProducts, double bestProduct, bool isFullScanMs, int step, float fontSize, int width, FullScanInfo fullScanInfo, PaneKey graphPaneKey) { if (tranPeakInfo == null) return; // Nothing to shade float end = tranPeakInfo.EndRetentionTime; float start = tranPeakInfo.StartRetentionTime; double[] allTimes; double[] allIntensities; info.AsArrays(out allTimes, out allIntensities); var peakTimes = new List<float>(); var peakIntensities = new List<float>(); for (int j = 0; j < allTimes.Length; j++) { if (start > allTimes[j]) continue; if (end < allTimes[j]) break; peakTimes.Add((float) allTimes[j]); peakIntensities.Add((float) allIntensities[j]); } if (peakIntensities.Count == 0) return; // Add peak area shading float[] peakTimesArray = peakTimes.ToArray(); info = new ChromatogramInfo(peakTimesArray, peakIntensities.ToArray()); var peakShadeItem = new ChromGraphItem(null, null, info, null, timeRegressionFunction, new bool[info.NumPeaks], dotProducts, bestProduct, isFullScanMs, false, step, ChromGraphItem.ColorSelected, fontSize, width, fullScanInfo); var peakShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, peakShadeItem); peakShadeCurveItem.Label.IsVisible = false; var lineItem = peakShadeCurveItem as LineItem; if (lineItem != null) { const int fillAlpha = 50; lineItem.Line.Fill = new Fill(Color.FromArgb(fillAlpha, lineItem.Color)); } // Add peak background shading float min = Math.Min(peakIntensities.First(), peakIntensities.Last()); info = new ChromatogramInfo(peakTimesArray, peakIntensities.Select(intensity => Math.Min(intensity, min)).ToArray()); var backgroundShadeItem = new ChromGraphItem(null, null, info, null, timeRegressionFunction, new bool[info.NumPeaks], dotProducts, bestProduct, isFullScanMs, false, step, Color.DarkGray, fontSize, 2, fullScanInfo); var backgroundShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, backgroundShadeItem); backgroundShadeCurveItem.Label.IsVisible = false; var lineItem2 = backgroundShadeCurveItem as LineItem; if (lineItem2 != null) { const int fillAlpha = 70; lineItem2.Line.Fill = new Fill(Color.FromArgb(fillAlpha, Color.Black)); } }
public ChromGraphItem(TransitionGroupDocNode transitionGroupNode, TransitionDocNode transition, ChromatogramInfo chromatogram, TransitionChromInfo tranPeakInfo, IRegressionFunction timeRegressionFunction, bool[] annotatePeaks, double[] dotProducts, double bestProduct, bool isFullScanMs, bool isSummary, int step, Color color, float fontSize, int width, FullScanInfo fullScanInfo = null) { TransitionGroupNode = transitionGroupNode; TransitionNode = transition; Chromatogram = chromatogram; TransitionChromInfo = tranPeakInfo; TimeRegressionFunction = timeRegressionFunction; Color = color; FullScanInfo = fullScanInfo; _step = step; _fontSpec = CreateFontSpec(color, fontSize); _width = width; _dotProducts = dotProducts; _bestProduct = bestProduct; _isFullScanMs = isFullScanMs; _isSummary = isSummary; _arrayLabelIndexes = new int[annotatePeaks.Length]; if (chromatogram == null) { _measuredTimes = new double[0]; _displayTimes = _measuredTimes; _intensities = new double[0]; } else { // Cache values early to avoid accessing slow enumerators // which show up under profiling. Chromatogram.AsArrays(out _measuredTimes, out _intensities); if (TimeRegressionFunction == null) { _displayTimes = _measuredTimes; } else { _displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray(); } // Add peak times to hash set for labeling int iLastStart = 0; for (int i = 0; i < chromatogram.NumPeaks; i++) { int maxIndex = -1; if (annotatePeaks[i]) { ChromPeak peak = chromatogram.GetPeak(i); maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart); } _arrayLabelIndexes[i] = maxIndex; if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex)) _annotatedTimes.Add(maxIndex, i); } // Calculate best peak index if (tranPeakInfo != null) { iLastStart = 0; _bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart); } } }
private void DisplayTransitions(IRegressionFunction timeRegressionFunction, TransitionDocNode nodeTranSelected, ChromatogramSet chromatograms, float mzMatchTolerance, TransitionGroupDocNode nodeGroup, ChromatogramGroupInfo chromGroupInfo, PaneKey graphPaneKey, DisplayTypeChrom displayType, ref double bestStartTime, ref double bestEndTime) { var fileId = chromatograms.FindFile(chromGroupInfo); // Get points for all transitions, and pick maximum peaks. ChromatogramInfo[] arrayChromInfo; var displayTrans = GetDisplayTransitions(nodeGroup, displayType).ToArray(); int numTrans = displayTrans.Length; int numSteps = 0; bool allowEmpty = false; if (IsSingleTransitionDisplay && nodeTranSelected != null) { if (!displayTrans.Contains(nodeTranSelected)) { arrayChromInfo = new ChromatogramInfo[0]; displayTrans = new TransitionDocNode[0]; numTrans = 0; } else { arrayChromInfo = chromGroupInfo.GetAllTransitionInfo((float) nodeTranSelected.Mz, mzMatchTolerance, chromatograms.OptimizationFunction); if (chromatograms.OptimizationFunction != null) { // Make sure the number of steps matches what will show up in the summary // graphs, or the colors won't match up. int numStepsExpected = chromatograms.OptimizationFunction.StepCount*2 + 1; if (arrayChromInfo.Length != numStepsExpected) { arrayChromInfo = ResizeArrayChromInfo(arrayChromInfo, numStepsExpected); allowEmpty = true; } } numTrans = arrayChromInfo.Length; displayTrans = new TransitionDocNode[numTrans]; for (int i = 0; i < numTrans; i++) displayTrans[i] = nodeTranSelected; } numSteps = numTrans/2; } else { arrayChromInfo = new ChromatogramInfo[numTrans]; for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; // Get chromatogram info for this transition arrayChromInfo[i] = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance); } } int bestPeakTran = -1; TransitionChromInfo tranPeakInfo = null; float maxPeakHeight = float.MinValue; int numPeaks = chromGroupInfo.NumPeaks; var maxPeakTrans = new int[numPeaks]; var maxPeakHeights = new float[numPeaks]; for (int i = 0; i < numPeaks; i++) maxPeakHeights[i] = float.MinValue; var transform = Transform; // Prepare arrays of values for library dot-product double[] expectedIntensities = null; double[][] peakAreas = null; bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1); bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1); bool isFullScanMs = DocumentUI.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs; if ((isFullScanMs && !isShowingMsMs && nodeGroup.HasIsotopeDist) || (!isFullScanMs && nodeGroup.HasLibInfo)) { expectedIntensities = new double[numTrans]; peakAreas = new double[numPeaks][]; for (int i = 0; i < numPeaks; i++) peakAreas[i] = new double[numTrans]; } // Find the transition with the maximum peak height for the best peak for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; int step = (numSteps > 0 ? i - numSteps : 0); var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, step); if (transitionChromInfo == null) continue; if (maxPeakHeight < transitionChromInfo.Height) { maxPeakHeight = transitionChromInfo.Height; bestPeakTran = i; tranPeakInfo = transitionChromInfo; } AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime); } for (int i = 0; i < numTrans; i++) { var nodeTran = displayTrans[i]; // Store library intensities for dot-product if (expectedIntensities != null) { if (isFullScanMs) expectedIntensities[i] = nodeTran.HasDistInfo ? nodeTran.IsotopeDistInfo.Proportion : 0; else expectedIntensities[i] = nodeTran.HasLibInfo ? nodeTran.LibInfo.Intensity : 0; } var info = arrayChromInfo[i]; if (info == null) continue; // Apply any active transform info.Transform(transform); for (int j = 0; j < numPeaks; j++) { var peak = info.GetPeak(j); // Exclude any peaks between the boundaries of the chosen peak. if (IntersectPeaks(peak, tranPeakInfo)) continue; // Store peak intensity for dot-product if (peakAreas != null) peakAreas[j][i] = peak.Area; // Keep track of which transition has the max height for each peak if (maxPeakHeights[j] < peak.Height) { maxPeakHeights[j] = peak.Height; maxPeakTrans[j] = i; } } } // Calculate library dot-products, if possible double[] dotProducts = null; double bestProduct = 0; int minProductTrans = isFullScanMs ? TransitionGroupDocNode.MIN_DOT_PRODUCT_MS1_TRANSITIONS : TransitionGroupDocNode.MIN_DOT_PRODUCT_TRANSITIONS; if (peakAreas != null && numTrans >= minProductTrans) { var tranGroupChromInfo = GetTransitionGroupChromInfo(nodeGroup, fileId, _chromIndex); double? dotProduct = null; if (tranGroupChromInfo != null) { dotProduct = isFullScanMs ? tranGroupChromInfo.IsotopeDotProduct : tranGroupChromInfo.LibraryDotProduct; } if (dotProduct.HasValue) { bestProduct = dotProduct.Value; var statExpectedIntensities = new Statistics(expectedIntensities); for (int i = 0; i < peakAreas.Length; i++) { var statPeakAreas = new Statistics(peakAreas[i]); double dotProductCurrent = statPeakAreas.NormalizedContrastAngleSqrt(statExpectedIntensities); // Only show products that are greater than the best peak product, // and by enough to be a significant improvement. Also the library product // on the group node is stored as a float, which means the version // hear calculated as a double can be larger, but really represent // the same number. if (dotProductCurrent > bestProduct && dotProductCurrent > 0.5 && dotProductCurrent - bestProduct > 0.05) { if (dotProducts == null) dotProducts = new double[numPeaks]; dotProducts[i] = dotProductCurrent; } } } } // Create graph items int iColor = 0; int lineWidth = LineWidth; float fontSize = FontSize; // We want the product ion colors to stay the same whether they are displayed: // 1. In a single pane with the precursor ions (Transitions -> All) // 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph) // 3. In a single pane by themselves (Transition -> Products) // We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors. var nodeDisplayType = GetDisplayType(DocumentUI, nodeGroup); int colorOffset = 0; if(displayType == DisplayTypeChrom.products && (nodeDisplayType != DisplayTypeChrom.single || (nodeDisplayType == DisplayTypeChrom.single && chromatograms.OptimizationFunction == null))) { colorOffset = GetDisplayTransitions(nodeGroup, DisplayTypeChrom.precursors).Count(); } for (int i = 0; i < numTrans; i++) { var info = arrayChromInfo[i]; if (info == null && !allowEmpty) continue; var nodeTran = displayTrans[i]; int step = numSteps != 0 ? i - numSteps : 0; Color color; bool shade = false; int width = lineWidth; if ((numSteps == 0 && ReferenceEquals(nodeTran, nodeTranSelected) || (numSteps > 0 && step == 0))) { color = ChromGraphItem.ColorSelected; shade = true; width++; } else { color = COLORS_LIBRARY[(iColor + colorOffset) % COLORS_LIBRARY.Length]; } TransitionChromInfo tranPeakInfoGraph = null; if (bestPeakTran == i) tranPeakInfoGraph = tranPeakInfo; var scanName = nodeTran.FragmentIonName; if (nodeTran.Transition.Charge != 1) // Positive singly charged is uninteresting scanName += Transition.GetChargeIndicator(nodeTran.Transition.Charge); if (nodeTran.Transition.MassIndex != 0) scanName += Environment.NewLine + Transition.GetMassIndexText(nodeTran.Transition.MassIndex); var fullScanInfo = new FullScanInfo { ChromInfo = info, ScanName = scanName }; if (fullScanInfo.ChromInfo != null && fullScanInfo.ChromInfo.ExtractionWidth > 0) _enableTrackingDot = true; var graphItem = new ChromGraphItem(nodeGroup, nodeTran, info, tranPeakInfoGraph, timeRegressionFunction, GetAnnotationFlags(i, maxPeakTrans, maxPeakHeights), dotProducts, bestProduct, isFullScanMs, false, step, color, fontSize, width, fullScanInfo); _graphHelper.AddChromatogram(graphPaneKey, graphItem); if (shade) { ShadeGraph(tranPeakInfo,info,timeRegressionFunction,dotProducts,bestProduct,isFullScanMs,step,fontSize,width,fullScanInfo,graphPaneKey); } iColor++; } var graphPane = _graphHelper.GetGraphPane(graphPaneKey); if (graphPane == null) _enableTrackingDot = false; if (_enableTrackingDot) { graphPane.CurveList.Insert(FULLSCAN_TRACKING_INDEX, CreateScanPoint(Color.Black)); graphPane.CurveList.Insert(FULLSCAN_SELECTED_INDEX, CreateScanPoint(Color.Red)); } }