private void SetSpectraUI(MsDataSpectrum[] spectra)
{
_msDataFileScanHelper.MsDataSpectra = spectra;
_heatMapData = null;
if (_msDataFileScanHelper.MsDataSpectra == null)
{
return;
}
// Find max values.
_maxMz = 0;
_maxIntensity = 0;
GetMaxMzIntensity(out _maxMz, out _maxIntensity);
_maxDriftTime = 0;
foreach (var spectrum in spectra)
{
_maxDriftTime = Math.Max(_maxDriftTime, spectrum.DriftTimeMsec ?? 0);
}
if (_zoomXAxis)
{
_zoomXAxis = false;
ZoomXAxis();
}
if (_zoomYAxis)
{
_zoomYAxis = false;
ZoomYAxis();
}
CreateGraph();
UpdateUI();
}
private void SetSpectraUI(MsDataSpectrum[] spectra)
{
_msDataFileScanHelper.MsDataSpectra = spectra;
_heatMapData = null;
if (_msDataFileScanHelper.MsDataSpectra == null)
{
return;
}
// Find max values.
_maxMz = 0;
_maxIntensity = 0;
GetMaxMzIntensity(out _maxMz, out _maxIntensity);
GetMaxMobility(out _maxIonMobility);
if (_zoomXAxis)
{
_zoomXAxis = false;
ZoomXAxis();
}
if (_zoomYAxis)
{
_zoomYAxis = false;
ZoomYAxis();
}
CreateGraph();
UpdateUI();
}
private void ShowHeatmap(double scanTime, int msLevel)
{
if (ionMobilityBinsByMsLevelAndScanTime.Count <= msLevel)
{
throw new ArgumentOutOfRangeException("msLevel", "no ion mobility bins for ms level " + msLevel);
}
var ionMobilityBinsByScanTime = ionMobilityBinsByMsLevelAndScanTime[msLevel];
if (!ionMobilityBinsByScanTime.Contains(scanTime))
{
throw new ArgumentOutOfRangeException("scanTime", "no ion mobility bins for scan time " + scanTime);
}
var heatmapGraphPane = heatmapGraphPaneByMsLevel[msLevel];
heatmapGraphPane.CurveList.Clear();
heatmapGraphPane.GraphObjList.Add(new TextObj("Loading...", 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 24
}
});
msGraphControl.Refresh();
var mobilityData = ionMobilityBinsByScanTime[scanTime];
var heatmapPointsTuple = heatmapPointsCache.GetOrAdd(mobilityData, o => o.Get3dSpectrum(), mobilityData);
var bounds = heatmapPointsTuple.Item2;
var g = msGraphControl.CreateGraphics();
var heatmapData = new HeatMapData(heatmapPointsTuple.Item1);
heatmapGraphPane.GraphObjList.Clear(); // remove "Loading..."
heatmapGraphPane.SetPoints(heatmapData, bounds.MinY, bounds.MaxY);
string isolationMzTitle = String.Empty;
if (msLevel + 1 == 2)
{
isolationMzTitle = " for isolation m/z " + String.Join(", ", isolationMzByScanTime[scanTime].Distinct());
}
heatmapGraphPane.Title.Text = String.Format("Ion Mobility Heatmap (ms{0} @ {1:F4} {3}{2})", msLevel + 1, scanTime, isolationMzTitle,
Properties.Settings.Default.TimeInMinutes ? "min." : "sec.");
setScale(heatmapGraphPane.XAxis.Scale, bounds.MinX, bounds.MaxX);
setScale(heatmapGraphPane.YAxis.Scale, bounds.MinY, bounds.MaxY);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
msGraphControl.Refresh();
}
//function for printing out HeatMap structure data
public static void printInfo(HeatMapData data)
{
double total_time = 0;
Console.WriteLine("\nts: " + data.ts);
Console.WriteLine("player_name: " + data.player_name);
Console.WriteLine("gridType: " + data.gridType);
foreach (var item in data.heatmap)
{
total_time += item.Value;
}
foreach (var item in data.heatmap)
{
Console.WriteLine("index: " + item.Key + " time % : " + (item.Value / total_time) * 100);
}
}
public float GetGrayColorRatio(int indexInitialDesired, int indexFinalDesired, int axisDivisionFactr, string requirementName)
{
float grayColorRatio;
HeatMapPoint correspondingHeatMapPoint = HeatMapData.Find(
delegate(HeatMapPoint heatMapPoint){
return((heatMapPoint.indexX == indexInitialDesired) && (heatMapPoint.indexY == indexFinalDesired));
});
grayColorRatio = correspondingHeatMapPoint.objectiveFunctionValues[requirementName];
grayColorRatio -= minimumValueOfObjectiveFunctions[requirementName];
if ((maximumValueOfObjectiveFunctions[requirementName] - minimumValueOfObjectiveFunctions[requirementName]) != 0)
{
grayColorRatio /= (maximumValueOfObjectiveFunctions[requirementName] - minimumValueOfObjectiveFunctions[requirementName]);
}
else
{
grayColorRatio = 0;
}
return(grayColorRatio);
}
/// <summary>
/// Registers Properties for Heat Map
/// </summary>
/// <param name="shape">Map Shape</param>
private void SetAdditionalData(MapShape shape)
{
ExtendedData data = shape.ExtendedData;
if (data != null)
{
if (!data.PropertySet.ContainsKey(COUNTRY_PERFORMANCE_FIELD))
{
data.PropertySet.RegisterProperty(COUNTRY_PERFORMANCE_FIELD, "CountryPerformance", typeof(int), 0);
}
if (!data.PropertySet.ContainsKey(COUNTRY_YTD_FIELD))
{
data.PropertySet.RegisterProperty(COUNTRY_YTD_FIELD, "CountryYTD", typeof(Decimal), Convert.ToDecimal(0));
}
if (!data.PropertySet.ContainsKey(BENCHMARK_YTD_FIELD))
{
data.PropertySet.RegisterProperty(BENCHMARK_YTD_FIELD, "BenchmarkYTD", typeof(Decimal), Convert.ToDecimal(0));
}
if (heatMapInfo != null)
{
string countryID = (string)shape.ExtendedData.GetValue("ISO_2DIGIT");
HeatMapData countryRecord = heatMapInfo.Where(r => r.CountryID == countryID).FirstOrDefault();
if (countryRecord != null)
{
shape.ExtendedData.SetValue(COUNTRY_PERFORMANCE_FIELD, (int)(countryRecord.CountryPerformance));
shape.ExtendedData.SetValue(COUNTRY_YTD_FIELD, countryRecord.CountryYTD);
shape.ExtendedData.SetValue(BENCHMARK_YTD_FIELD, countryRecord.BenchmarkYTD);
AddColorizerToInformationLayer(shape, countryRecord);
}
else
{
shape.ExtendedData.SetValue(COUNTRY_PERFORMANCE_FIELD, null);
shape.ExtendedData.SetValue(COUNTRY_YTD_FIELD, null);
shape.ExtendedData.SetValue(BENCHMARK_YTD_FIELD, null);
AddTransparentColorizerToInformationLayer(shape);
}
}
}
}
/// <summary>
/// Adding Colour to Each Shape
/// </summary>
/// <param name="shape">Shape</param>
/// <param name="countryRecord">Country record of type heat map data</param>
private void AddColorizerToInformationLayer(MapShape shape, HeatMapData countryRecord)
{
if ((int)(countryRecord.CountryPerformance) == 3)
{
shape.Fill = new SolidColorBrush(Colors.Green);
}
else
if ((int)(countryRecord.CountryPerformance) == 1)
{
shape.Fill = new SolidColorBrush(Colors.Red);
}
else
if ((int)(countryRecord.CountryPerformance) == 2)
{
shape.Fill = new SolidColorBrush(Colors.Gray);
}
else
if ((int)(countryRecord.CountryPerformance) == 0)
{
shape.Fill = new SolidColorBrush(Colors.White);
}
}
//aggregatorFunction used in TimeWindow based aggregation
private static HeatMapData aggregatorFunction(HeatMapData seed, TimeInCell curr,
IList <TimeInCell> expList, long count)
{
HeatMapData new_seed = new HeatMapData {
ts = curr.ts, player_name = curr.player_name,
gridType = curr.gridType, heatmap = seed.heatmap
};
foreach (var item in expList)
{
if (item.time_in_cell != -999)
{
if (new_seed.heatmap.ContainsKey(item.prev_index))
{
new_seed.heatmap[item.prev_index] -= item.time_in_cell;
if (new_seed.heatmap[item.prev_index] <= 0)
{
new_seed.heatmap.Remove(item.prev_index);
}
}
else
{
Console.WriteLine("HeatMapProcessor: Attempt to access non-existent key");
}
}
}
if (curr.time_in_cell != -999)
{
if (new_seed.heatmap.ContainsKey(curr.prev_index))
{
new_seed.heatmap[curr.prev_index] += curr.time_in_cell;
}
else
{
new_seed.heatmap.Add(curr.prev_index, curr.time_in_cell);
}
}
return(new_seed);
}
private void SetSpectraUI(MsDataSpectrum[] spectra)
{
_msDataFileScanHelper.MsDataSpectra = spectra;
_heatMapData = null;
if (_msDataFileScanHelper.MsDataSpectra == null)
{
return;
}
foreach (var spectrum in spectra)
{
if (spectrum.IonMobilities != null)
{
ArrayUtil.Sort(spectrum.Mzs, spectrum.Intensities, spectrum.IonMobilities);
}
}
// Find max values.
_maxMz = 0;
_maxIntensity = 0;
GetMaxMzIntensity(out _maxMz, out _maxIntensity);
GetMaxMobility(out _maxIonMobility);
if (_zoomXAxis)
{
_zoomXAxis = false;
ZoomXAxis();
}
if (_zoomYAxis)
{
_zoomYAxis = false;
ZoomYAxis();
}
CreateGraph();
UpdateUI();
}
public GraphData(SrmDocument document, GraphData dataPrevious, int resultIndex,
bool bestResult, PointsTypeMassError pointsType)
{
_document = document;
_resultIndex = resultIndex;
_replicateDisplay = ShowReplicate;
int[,] counts2D = EMPTY_COUNTS;
_displayType = MassErrorGraphController.HistogramDisplayType;
_binSizePpm = Settings.Default.MassErorrHistogramBinSize;
_transition = MassErrorGraphController.HistogramTransiton;
_xAxis = MassErrorGraphController.Histogram2DXAxis;
_pointsType = pointsType;
if (_pointsType == PointsTypeMassError.targets_1FDR && !document.Settings.PeptideSettings.Integration.PeakScoringModel.IsTrained)
{
_pointsType = PointsTypeMassError.targets;
}
bool decoys = pointsType == PointsTypeMassError.decoys;
bool precursors = _displayType == DisplayTypeMassError.precursors;
while (ReferenceEquals(counts2D, EMPTY_COUNTS))
{
if (_maxMass != double.MinValue)
{
counts2D = new int[xAxisBins, (int)((_maxMass - _minMass) / _binSizePpm + 1)];
}
foreach (var nodePep in document.Molecules)
{
if (decoys != nodePep.IsDecoy)
{
continue;
}
var replicateIndex = bestResult && nodePep.BestResult != -1 ? nodePep.BestResult : resultIndex;
foreach (var nodeGroup in nodePep.TransitionGroups)
{
foreach (var nodeTran in nodeGroup.Transitions)
{
if (precursors != nodeTran.IsMs1)
{
continue;
}
var mz = nodeTran.Mz.Value;
if (replicateIndex >= 0)
{
AddChromInfo(nodeGroup, nodeTran, replicateIndex, mz, counts2D);
}
else
{
for (int i = 0; i < nodeTran.Results.Count; i++)
{
AddChromInfo(nodeGroup, nodeTran, i, mz, counts2D);
}
}
}
}
}
// No values. Leave _maxCount == 0
if (_maxMass == double.MinValue)
{
return;
}
}
var points = new List <Point3D>();
for (int x = 0; x < counts2D.GetLength(0); x++)
{
for (int y = 0; y < counts2D.GetLength(1); y++)
{
int count = counts2D[x, y];
if (count > 0)
{
double binSizeX = (_maxX - _minX) / xAxisBins;
double xPoint = x * binSizeX + _minX + binSizeX / 2;
double yPoint = y * _binSizePpm + _minMass + _binSizePpm / 2;
points.Add(new Point3D(xPoint, yPoint, count));
}
_maxCount = Math.Max(_maxCount, count);
}
}
_heatMapData = new HeatMapData(points);
}
private void ShowHeatmap(double scanTime, int msLevel)
{
if (ionMobilityBinsByMsLevelAndScanTime.Count <= msLevel)
{
throw new ArgumentOutOfRangeException("msLevel", "no ion mobility bins for ms level " + msLevel);
}
var ionMobilityBinsByScanTime = ionMobilityBinsByMsLevelAndScanTime[msLevel];
if (!ionMobilityBinsByScanTime.Contains(scanTime))
{
throw new ArgumentOutOfRangeException("scanTime", "no ion mobility bins for scan time " + scanTime);
}
var ionMobilityBins = ionMobilityBinsByScanTime[scanTime];
var heatmapPoints = new List <Point3D>(ionMobilityBins.Count);
var heatmapGraphPane = heatmapGraphPaneByMsLevel[msLevel];
heatmapGraphPane.CurveList.Clear();
heatmapGraphPane.GraphObjList.Add(new TextObj("Loading...", 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 24
}
});
msGraphControl.Refresh();
var bounds = heatmapBoundsByMsLevel[msLevel];
foreach (var bin in ionMobilityBins)
{
var spectrum = source.GetMassSpectrum(bin.BinIndex);
var points = spectrum.Points;
for (int j = 0; j < points.Count; ++j)
{
double mz = points[j].X;
double intensity = points[j].Y;
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, bin.IonMobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, bin.IonMobility);
heatmapPoints.Add(new Point3D(mz, bin.IonMobility, intensity));
}
}
var g = msGraphControl.CreateGraphics();
var heatmapData = new HeatMapData(heatmapPoints);
heatmapGraphPane.GraphObjList.Clear(); // remove "Loading..."
heatmapGraphPane.SetPoints(heatmapData, bounds.MinY, bounds.MaxY);
heatmapGraphPane.Title.Text = String.Format("Ion Mobility Heatmap (ms{0} @ {1:F4} min.)", msLevel + 1, scanTime);
setScale(heatmapGraphPane.XAxis.Scale, bounds.MinX, bounds.MaxX);
setScale(heatmapGraphPane.YAxis.Scale, bounds.MinY, bounds.MaxY);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
msGraphControl.Refresh();
}
private void ShowHeatmaps()
{
var dgv = source.SpectrumListForm.GridView;
var scanTimeColumn = dgv.Columns["ScanTime"];
var msLevelColumn = dgv.Columns["MsLevel"];
var heatmapPointsByMsLevel = new List <List <Point3D> >(dgv.RowCount);
var msLevels = new Set <int>();
for (int i = 0; i < dgv.RowCount; ++i)
{
msLevels.Add((int)dgv[msLevelColumn.Index, i].Value - 1);
}
while (heatmapPointsByMsLevel.Count <= msLevels.Max)
{
heatmapPointsByMsLevel.Add(new List <Point3D>());
}
var peakPicker = new pwiz.CLI.analysis.SpectrumList_PeakPicker(source.Source.MSDataFile.run.spectrumList, new pwiz.CLI.analysis.CwtPeakDetector(1, 0.5), true, new int[] { 1 });
for (int i = 0; i < dgv.RowCount; ++i)
{
int msLevel = (int)dgv[msLevelColumn.Index, i].Value - 1;
var heatmapGraphPane = heatmapGraphPaneByMsLevel[msLevel];
var heatmapPoints = heatmapPointsByMsLevel[msLevel];
if (i == 0 || i + 1 == dgv.RowCount || ((i + 1) % 1000) == 0)
{
heatmapGraphPane.CurveList.Clear();
heatmapGraphPane.GraphObjList.Add(new TextObj(String.Format("Loading {0}/{1}", i + 1, dgv.RowCount), 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 24
}
});
msGraphControl.Refresh();
}
Application.DoEvents();
var bounds = heatmapBoundsByMsLevel[msLevel];
var spectrum = source.GetMassSpectrum(source.Source.Spectra[i].Index, peakPicker);
double scanTime = (double)dgv[scanTimeColumn.Index, i].Value;
var points = spectrum.Points;
for (int j = 0; j < points.Count; ++j)
{
double intensity = points[j].Y;
if (intensity == 0)
{
continue;
}
double mz = points[j].X;
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, scanTime);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, scanTime);
heatmapPoints.Add(new Point3D(mz, scanTime, intensity));
}
}
var g = msGraphControl.CreateGraphics();
foreach (int msLevel in msLevels)
{
var bounds = heatmapBoundsByMsLevel[msLevel];
var heatmapData = new HeatMapData(heatmapPointsByMsLevel[msLevel]);
var heatmapGraphPane = heatmapGraphPaneByMsLevel[msLevel];
heatmapGraphPane.GraphObjList.Clear(); // remove "Loading..."
heatmapGraphPane.SetPoints(heatmapData, bounds.MinY, bounds.MaxY);
heatmapGraphPane.Title.Text = String.Format("Time to m/z Heatmap (ms{0})", msLevel + 1);
setScale(heatmapGraphPane.XAxis.Scale, bounds.MinX, bounds.MaxX);
setScale(heatmapGraphPane.YAxis.Scale, bounds.MinY, bounds.MaxY);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
msGraphControl.Refresh();
}
}
public override void UpdateGraph(bool selectionChanged)
{
if (!GraphSummary.DocumentUIContainer.DocumentUI.Settings.HasResults)
{
_areaCVGraphData = null;
return;
}
var settings = new AreaCVGraphData.AreaCVGraphSettings(GraphSummary.Type);
_document = GraphSummary.DocumentUIContainer.DocumentUI;
_percentage = !Settings.Default.AreaCVShowDecimals;
_decimals = _percentage ? 1 : 3;
CurveList.Clear();
var gotData = _cache.TryGet(_document, settings, DataCallback, out _areaCVGraphData);
if (!gotData)
{
Title.Text = Resources.AreaCVHistogram2DGraphPane_UpdateGraph_Calculating____;
return;
}
if (!_areaCVGraphData.IsValid)
{
Title.Text = Resources.AreaCVHistogram2DGraphPane_Draw_Not_enough_data;
return;
}
var factor = AreaGraphController.GetAreaCVFactorToDecimal();
Title.Text = string.Empty;
YAxis.Title.Text = Resources.AreaCVHistogram2DGraphPane_UpdateGraph_CV + (_percentage ? @" (%)" : string.Empty);
XAxis.Title.Text = Resources.AreaCvHistogram2DGraphPane_UpdateGraph_Log10_Mean_Area;
XAxis.Scale.MinAuto = XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = YAxis.Scale.MaxAuto = false;
XAxis.Scale.Min = Math.Max(0, double.IsNaN(Settings.Default.AreaCVMinLog10Area) ? _areaCVGraphData.MinMeanArea : Settings.Default.AreaCVMinLog10Area);
XAxis.Scale.Max = double.IsNaN(Settings.Default.AreaCVMaxLog10Area) ? _areaCVGraphData.MaxMeanArea : Settings.Default.AreaCVMaxLog10Area;
YAxis.Scale.Min = 0.0;
YAxis.Scale.Max = double.IsNaN(Settings.Default.AreaCVMaxCV) ? _areaCVGraphData.MaxCV * factor : Settings.Default.AreaCVMaxCV;
AxisChange();
var points = _areaCVGraphData.Data
.Select(d => new HeatMapData.TaggedPoint3D(new Point3D(d.MeanArea, d.CV * factor, d.Frequency), d))
.ToList();
Items = points.Count; // Because heatmaps can't be trusted to have a consistent number of points on all monitors
var heatMapData = new HeatMapData(points);
HeatMapGraphPane.GraphHeatMap(this, heatMapData, 17, 2, (float)(_areaCVGraphData.MinCV * factor), (float)(_areaCVGraphData.MaxCV * factor), Settings.Default.AreaCVLogScale, 0);
var unit = _percentage ? @"%" : string.Empty;
if (Settings.Default.AreaCVShowMedianCV)
{
string text = string.Format(Resources.AreaCVHistogram2DGraphPane_UpdateGraph_Median___0_, HistogramHelper.FormatDouble(_areaCVGraphData.MedianCV * factor, _decimals) + unit);
_lineItems[0] = AddLineItem(text, XAxis.Scale.Min, XAxis.Scale.Max, _areaCVGraphData.MedianCV * factor, _areaCVGraphData.MedianCV * factor, Color.Blue);
CurveList.Insert(0, _lineItems[0]);
}
if (Settings.Default.AreaCVShowCVCutoff)
{
string text = string.Format(Resources.AreaCVHistogramGraphPane_UpdateGraph_Below__0____1_, Settings.Default.AreaCVCVCutoff + unit,
HistogramHelper.FormatDouble(_areaCVGraphData.BelowCVCutoff * factor, _decimals) +
unit);
_lineItems[1] = AddLineItem(text, XAxis.Scale.Min, XAxis.Scale.Max, Settings.Default.AreaCVCVCutoff, Settings.Default.AreaCVCVCutoff, Color.Red);
CurveList.Insert(0, _lineItems[1]);
}
}
public void AddPoint(HeatMapPoint heatMapPoint)
{
HeatMapData.Add(heatMapPoint);
}
private void ShowHeatmap(double scanTime, int msLevel)
{
if (ionMobilityBinsByMsLevelAndScanTime.Count <= msLevel)
{
throw new ArgumentOutOfRangeException("msLevel", "no ion mobility bins for ms level " + msLevel);
}
var ionMobilityBinsByScanTime = ionMobilityBinsByMsLevelAndScanTime[msLevel];
if (!ionMobilityBinsByScanTime.Contains(scanTime))
{
throw new ArgumentOutOfRangeException("scanTime", "no ion mobility bins for scan time " + scanTime);
}
var ionMobilityBins = ionMobilityBinsByScanTime[scanTime];
var heatmapPoints = new List <Point3D>(ionMobilityBins.Count);
var heatmapGraphPane = heatmapGraphPaneByMsLevel[msLevel];
heatmapGraphPane.CurveList.Clear();
heatmapGraphPane.GraphObjList.Add(new TextObj("Loading...", 0.5, 0.5, CoordType.ChartFraction)
{
FontSpec = new FontSpec {
Border = new Border {
IsVisible = false
}, IsBold = true, Size = 24
}
});
msGraphControl.Refresh();
var mainSpectrumList = source.Source.MSDataFile.run.spectrumList;
var bounds = heatmapBoundsByMsLevel[msLevel];
int lastBinIndex = -1;
foreach (var bin in ionMobilityBins)
{
// skip bins where the spectrum is the same as the last bin (that spectrum's points were added from its mobility array)
if (bin.BinIndex == lastBinIndex)
{
continue;
}
lastBinIndex = bin.BinIndex;
var s = mainSpectrumList.spectrum(bin.BinIndex, true);
var mzArray = s.getMZArray().data;
var intensityArray = s.getIntensityArray().data;
var mobilityBDA = s.getArrayByCVID(pwiz.CLI.cv.CVID.MS_mean_drift_time_array);
if (mobilityBDA == null)
{
mobilityBDA = s.getArrayByCVID(pwiz.CLI.cv.CVID.MS_mean_inverse_reduced_ion_mobility_array);
}
if (mobilityBDA != null)
{
var mobilityArray = mobilityBDA.data;
for (int j = 0, end = mzArray.Count; j < end; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
double mobility = mobilityArray[j];
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, mobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, mobility);
heatmapPoints.Add(new Point3D(mz, mobility, intensity));
}
}
else
{
for (int j = 0, end = mzArray.Count; j < end; ++j)
{
double mz = mzArray[j];
double intensity = intensityArray[j];
bounds.MinX = Math.Min(bounds.MinX, mz);
bounds.MinY = Math.Min(bounds.MinY, bin.IonMobility);
bounds.MaxX = Math.Max(bounds.MaxX, mz);
bounds.MaxY = Math.Max(bounds.MaxY, bin.IonMobility);
heatmapPoints.Add(new Point3D(mz, bin.IonMobility, intensity));
}
}
}
var g = msGraphControl.CreateGraphics();
var heatmapData = new HeatMapData(heatmapPoints);
heatmapGraphPane.GraphObjList.Clear(); // remove "Loading..."
heatmapGraphPane.SetPoints(heatmapData, bounds.MinY, bounds.MaxY);
heatmapGraphPane.Title.Text = String.Format("Ion Mobility Heatmap (ms{0} @ {1:F4} min.)", msLevel + 1, scanTime);
setScale(heatmapGraphPane.XAxis.Scale, bounds.MinX, bounds.MaxX);
setScale(heatmapGraphPane.YAxis.Scale, bounds.MinY, bounds.MaxY);
heatmapGraphPane.AxisChange(g);
heatmapGraphPane.SetScale(g);
msGraphControl.Refresh();
}
/// <summary>
/// Create an ion mobility heat map graph.
/// </summary>
private void CreateIonMobilityHeatmap()
{
GraphPane.YAxis.Title.Text = IonMobilityFilter.IonMobilityUnitsL10NString(_msDataFileScanHelper.IonMobilityUnits);
graphControl.IsEnableVZoom = graphControl.IsEnableVPan = true;
if (_heatMapData == null)
{
var points = new List <Point3D>(5000);
foreach (var scan in _msDataFileScanHelper.MsDataSpectra)
{
if (!scan.IonMobility.HasValue && scan.IonMobilities == null)
{
continue;
}
for (int j = 0; j < scan.Mzs.Length; j++)
{
double mobilityValue = scan.IonMobilities != null
? scan.IonMobilities[j]
: scan.IonMobility.Mobility.Value;
points.Add(new Point3D(scan.Mzs[j], mobilityValue, scan.Intensities[j]));
}
}
_heatMapData = new HeatMapData(points);
}
double minDrift;
double maxDrift;
_msDataFileScanHelper.GetIonMobilityRange(out minDrift, out maxDrift, _msDataFileScanHelper.Source); // There may be a different drift time filter for products in Waters
if (minDrift > 0 && maxDrift < double.MaxValue)
{
// Add gray shaded box behind heat points.
var driftTimeBox = new BoxObj(
0.0,
maxDrift,
1.0,
maxDrift - minDrift,
Color.Transparent,
Color.FromArgb(50, Color.Gray))
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale },
ZOrder = ZOrder.F_BehindGrid,
IsClippedToChartRect = true,
};
GraphPane.GraphObjList.Add(driftTimeBox);
// Add outline in front of heat points, so you can tell where the limits are in a dense graph.
var driftTimeOutline = new BoxObj(
0.0,
maxDrift,
1.0,
maxDrift - minDrift,
Color.FromArgb(50, Color.DarkViolet),
Color.Transparent)
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale },
ZOrder = ZOrder.C_BehindChartBorder,
IsClippedToChartRect = true,
Border = new Border(Color.FromArgb(100, Color.DarkViolet), 2)
};
GraphPane.GraphObjList.Add(driftTimeOutline);
}
if (!Settings.Default.FilterIonMobilityFullScan)
{
minDrift = 0;
maxDrift = double.MaxValue;
}
var heatMapGraphPane = (HeatMapGraphPane)GraphPane;
heatMapGraphPane.SetPoints(_heatMapData, minDrift, maxDrift);
}
//function for printing out HeatMap structure data
public static void printInfo(HeatMapData data)
{
double total_time = 0;
Console.WriteLine("\nts: " + data.ts);
Console.WriteLine("player_name: " + data.player_name);
Console.WriteLine("gridType: " + data.gridType);
foreach (var item in data.heatmap)
total_time += item.Value;
foreach (var item in data.heatmap)
Console.WriteLine("index: " + item.Key + " time % : " + (item.Value / total_time) * 100);
}
//aggregatorFunction used in TimeWindow based aggregation
private static HeatMapData aggregatorFunction(HeatMapData seed, TimeInCell curr,
IList<TimeInCell> expList, long count)
{
HeatMapData new_seed = new HeatMapData { ts = curr.ts, player_name = curr.player_name,
gridType=curr.gridType, heatmap = seed.heatmap};
foreach(var item in expList)
{
if (item.time_in_cell != -999)
{
if (new_seed.heatmap.ContainsKey(item.prev_index))
{
new_seed.heatmap[item.prev_index] -= item.time_in_cell;
if (new_seed.heatmap[item.prev_index] <= 0)
new_seed.heatmap.Remove(item.prev_index);
}
else
{
Console.WriteLine("HeatMapProcessor: Attempt to access non-existent key");
}
}
}
if (curr.time_in_cell != -999)
{
if (new_seed.heatmap.ContainsKey(curr.prev_index))
new_seed.heatmap[curr.prev_index] += curr.time_in_cell;
else
new_seed.heatmap.Add(curr.prev_index, curr.time_in_cell);
}
return new_seed;
}
