private void RemoveZeroesAtFrontAndBack(clsChromatogramInfo chromatogramInfo)
{
const int MAX_POINTS_TO_CHECK = 100;
var pointsChecked = 0;
// See if the last few values are zero, but the data before them is non-zero
// If this is the case, remove the final entries
var indexNonZeroValue = -1;
var zeroPointCount = 0;
for (var index = chromatogramInfo.ScanCount - 1; index >= 0; index += -1)
{
if (Math.Abs(chromatogramInfo.GetDataPoint(index).Intensity) < float.Epsilon)
{
zeroPointCount += 1;
}
else
{
indexNonZeroValue = index;
break;
}
pointsChecked += 1;
if (pointsChecked >= MAX_POINTS_TO_CHECK)
{
break;
}
}
if (zeroPointCount > 0 && indexNonZeroValue >= 0)
{
chromatogramInfo.RemoveRange(indexNonZeroValue + 1, zeroPointCount);
}
// Now check the first few values
indexNonZeroValue = -1;
zeroPointCount = 0;
for (var index = 0; index <= chromatogramInfo.ScanCount - 1; index++)
{
if (Math.Abs(chromatogramInfo.GetDataPoint(index).Intensity) < float.Epsilon)
{
zeroPointCount += 1;
}
else
{
indexNonZeroValue = index;
break;
}
pointsChecked += 1;
if (pointsChecked >= MAX_POINTS_TO_CHECK)
{
break;
}
}
if (zeroPointCount > 0 && indexNonZeroValue >= 0)
{
chromatogramInfo.RemoveRange(0, indexNonZeroValue);
}
}
/// <summary>
/// Clear BPI and TIC data
/// </summary>
public void Reset()
{
if (mBPI == null)
{
mBPI = new clsChromatogramInfo();
mTIC = new clsChromatogramInfo();
}
else
{
mBPI.Initialize();
mTIC.Initialize();
}
mRecentFiles.Clear();
}
private clsPlotContainerBase InitializePlot(
clsChromatogramInfo chromatogramData,
string plotTitle,
int msLevelFilter,
string xAxisLabel,
string yAxisLabel,
bool autoMinMaxY,
bool yAxisExponentialNotation)
{
if (PlotWithPython)
{
return(InitializePythonPlot(chromatogramData, plotTitle, msLevelFilter, xAxisLabel, yAxisLabel, autoMinMaxY, yAxisExponentialNotation));
}
else
{
return(InitializeOxyPlot(chromatogramData, plotTitle, msLevelFilter, xAxisLabel, yAxisLabel, autoMinMaxY, yAxisExponentialNotation));
}
}
private void ValidateMSLevel(clsChromatogramInfo chromatogramInfo)
{
var msLevelDefined = false;
for (var index = 0; index <= chromatogramInfo.ScanCount - 1; index++)
{
if (chromatogramInfo.GetDataPoint(index).MSLevel > 0)
{
msLevelDefined = true;
break;
}
}
if (!msLevelDefined)
{
// Set the MSLevel to 1 for all scans
for (var index = 0; index <= chromatogramInfo.ScanCount - 1; index++)
{
chromatogramInfo.GetDataPoint(index).MSLevel = 1;
}
}
}
private void ValidateMSLevel(clsChromatogramInfo objChrom)
{
var blnMSLevelDefined = false;
for (var intIndex = 0; intIndex <= objChrom.ScanCount - 1; intIndex++)
{
if (objChrom.GetDataPoint(intIndex).MSLevel > 0)
{
blnMSLevelDefined = true;
break;
}
}
if (!blnMSLevelDefined)
{
// Set the MSLevel to 1 for all scans
for (var intIndex = 0; intIndex <= objChrom.ScanCount - 1; intIndex++)
{
objChrom.GetDataPoint(intIndex).MSLevel = 1;
}
}
}
/// <summary>
/// Plots a BPI or TIC chromatogram
/// </summary>
/// <param name="chromatogramData">Data to display</param>
/// <param name="plotTitle">Title of the plot</param>
/// <param name="msLevelFilter">0 to use all of the data, 1 to use data from MS scans, 2 to use data from MS2 scans, etc.</param>
/// <param name="xAxisLabel"></param>
/// <param name="yAxisLabel"></param>
/// <param name="autoMinMaxY"></param>
/// <param name="yAxisExponentialNotation"></param>
/// <returns>Python PlotContainer</returns>
private clsPythonPlotContainer InitializePythonPlot(
clsChromatogramInfo chromatogramData,
string plotTitle,
int msLevelFilter,
string xAxisLabel,
string yAxisLabel,
bool autoMinMaxY,
bool yAxisExponentialNotation)
{
double scanTimeMax = 0;
double maxIntensity = 0;
// Instantiate the list to track the data points
var points = new List <DataPoint>();
foreach (var dataPoint in chromatogramData.Scans)
{
if (msLevelFilter != 0 && dataPoint.MSLevel != msLevelFilter &&
!(msLevelFilter == 2 && dataPoint.MSLevel >= 2))
{
continue;
}
points.Add(new DataPoint(dataPoint.ScanNum, dataPoint.Intensity));
if (dataPoint.TimeMinutes > scanTimeMax)
{
scanTimeMax = dataPoint.TimeMinutes;
}
if (dataPoint.Intensity > maxIntensity)
{
maxIntensity = dataPoint.Intensity;
}
}
if (points.Count == 0)
{
// Nothing to plot
var emptyContainer = new clsPythonPlotContainer2D();
return(emptyContainer);
}
var plotContainer = new clsPythonPlotContainer2D(plotTitle, xAxisLabel, yAxisLabel)
{
DeleteTempFiles = DeleteTempFiles
};
if (yAxisExponentialNotation)
{
plotContainer.YAxisInfo.StringFormat = clsAxisInfo.EXPONENTIAL_FORMAT;
}
plotContainer.SetData(points);
// Update the axis format codes if the data values are small or the range of data is small
// Assume the X axis is plotting integers
var xVals = (from item in points select item.X).ToList();
clsPlotUtilities.GetAxisFormatInfo(xVals, true, plotContainer.XAxisInfo);
// Assume the Y axis is plotting doubles
var yVals = (from item in points select item.Y).ToList();
clsPlotUtilities.GetAxisFormatInfo(yVals, false, plotContainer.YAxisInfo);
// Possibly add a label showing the maximum elution time
if (scanTimeMax > 0)
{
string caption;
if (scanTimeMax < 2)
{
caption = Math.Round(scanTimeMax, 2).ToString("0.00") + " minutes";
}
else if (scanTimeMax < 10)
{
caption = Math.Round(scanTimeMax, 1).ToString("0.0") + " minutes";
}
else
{
caption = Math.Round(scanTimeMax, 0).ToString("0") + " minutes";
}
plotContainer.AnnotationBottomRight = caption;
}
// Override the auto-computed Y axis range
if (autoMinMaxY)
{
// Auto scale
}
else
{
plotContainer.XAxisInfo.SetRange(0, maxIntensity);
}
return(plotContainer);
}
/// <summary>
/// Plots a BPI or TIC chromatogram
/// </summary>
/// <param name="chromatogramData">Data to display</param>
/// <param name="plotTitle">Title of the plot</param>
/// <param name="msLevelFilter">0 to use all of the data, 1 to use data from MS scans, 2 to use data from MS2 scans, etc.</param>
/// <param name="xAxisLabel"></param>
/// <param name="yAxisLabel"></param>
/// <param name="autoMinMaxY"></param>
/// <param name="yAxisExponentialNotation"></param>
/// <returns>OxyPlot PlotContainer</returns>
private clsPlotContainer InitializeOxyPlot(
clsChromatogramInfo chromatogramData,
string plotTitle,
int msLevelFilter,
string xAxisLabel,
string yAxisLabel,
bool autoMinMaxY,
bool yAxisExponentialNotation)
{
var minScan = int.MaxValue;
var maxScan = 0;
double scanTimeMax = 0;
double maxIntensity = 0;
// Instantiate the list to track the data points
var points = new List <DataPoint>();
foreach (var dataPoint in chromatogramData.Scans)
{
if (msLevelFilter != 0 && dataPoint.MSLevel != msLevelFilter &&
!(msLevelFilter == 2 && dataPoint.MSLevel >= 2))
{
continue;
}
points.Add(new DataPoint(dataPoint.ScanNum, dataPoint.Intensity));
if (dataPoint.TimeMinutes > scanTimeMax)
{
scanTimeMax = dataPoint.TimeMinutes;
}
if (dataPoint.ScanNum < minScan)
{
minScan = dataPoint.ScanNum;
}
if (dataPoint.ScanNum > maxScan)
{
maxScan = dataPoint.ScanNum;
}
if (dataPoint.Intensity > maxIntensity)
{
maxIntensity = dataPoint.Intensity;
}
}
if (points.Count == 0)
{
// Nothing to plot
var emptyContainer = new clsPlotContainer(new PlotModel(), mWriteDebug, mDataSource);
emptyContainer.WriteDebugLog("points.Count == 0 in InitializeOxyPlot for plot " + plotTitle);
return(emptyContainer);
}
// Round maxScan down to the nearest multiple of 10
maxScan = (int)Math.Ceiling(maxScan / 10.0) * 10;
// Multiple maxIntensity by 2% and then round up to the nearest integer
maxIntensity = Math.Ceiling(maxIntensity * 1.02);
var myPlot = clsOxyPlotUtilities.GetBasicPlotModel(plotTitle, xAxisLabel, yAxisLabel);
if (yAxisExponentialNotation)
{
myPlot.Axes[1].StringFormat = clsAxisInfo.EXPONENTIAL_FORMAT;
}
AddOxyPlotSeries(myPlot, points);
// Update the axis format codes if the data values are small or the range of data is small
var xVals = (from item in points select item.X).ToList();
clsOxyPlotUtilities.UpdateAxisFormatCodeIfSmallValues(myPlot.Axes[0], xVals, true);
var yVals = (from item in points select item.Y).ToList();
clsOxyPlotUtilities.UpdateAxisFormatCodeIfSmallValues(myPlot.Axes[1], yVals, false);
var plotContainer = new clsPlotContainer(myPlot, mWriteDebug, mDataSource)
{
FontSizeBase = clsPlotContainer.DEFAULT_BASE_FONT_SIZE
};
plotContainer.WriteDebugLog(string.Format("Instantiated plotContainer for plot {0}: {1} data points", plotTitle, points.Count));
// Possibly add a label showing the maximum elution time
if (scanTimeMax > 0)
{
string caption;
if (scanTimeMax < 2)
{
caption = Math.Round(scanTimeMax, 2).ToString("0.00") + " minutes";
}
else if (scanTimeMax < 10)
{
caption = Math.Round(scanTimeMax, 1).ToString("0.0") + " minutes";
}
else
{
caption = Math.Round(scanTimeMax, 0).ToString("0") + " minutes";
}
plotContainer.AnnotationBottomRight = caption;
// Alternative method is to add a TextAnnotation, but these are inside the main plot area
// and are tied to a data point
//
// var scanTimeMaxText = new OxyPlot.Annotations.TextAnnotation
// {
// TextRotation = 0,
// Text = caption,
// Stroke = OxyColors.Black,
// StrokeThickness = 2,
// FontSize = clsPlotContainer.DEFAULT_BASE_FONT_SIZE
// };
//
// scanTimeMaxText.TextPosition = new DataPoint(maxScan, 0);
// myPlot.Annotations.Add(scanTimeMaxText);
}
// Override the auto-computed X axis range
if (minScan == maxScan)
{
myPlot.Axes[0].Minimum = minScan - 1;
myPlot.Axes[0].Maximum = minScan + 1;
}
else
{
myPlot.Axes[0].Minimum = 0;
if (maxScan == 0)
{
myPlot.Axes[0].Maximum = 1;
}
else
{
myPlot.Axes[0].Maximum = maxScan;
}
}
// Assure that we don't see ticks between scan numbers
clsOxyPlotUtilities.ValidateMajorStep(myPlot.Axes[0]);
// Override the auto-computed Y axis range
if (autoMinMaxY)
{
// Auto scale
}
else
{
myPlot.Axes[1].Minimum = 0;
myPlot.Axes[1].Maximum = maxIntensity;
}
// Hide the legend
myPlot.IsLegendVisible = false;
return(plotContainer);
}
