/// <summary>
/// Gets the interval average of all spectrums.
/// </summary>
/// <returns>Interval</returns>
private double GetAverageInterval()
{
double sum = 0;
int count = 0;
for (int i = 0; i < _param.GetXYDataNum(); i++)
{
ClrDataPoints xydata = _param.GetXYData(i);
if (xydata.getLength() <= 1)
{
continue;
}
uint length = xydata.getLength();
for (uint j = 1; j < length; j++)
{
double distance = Math.Abs(xydata.getX(j) - xydata.getX(j - 1));
if (distance == 0)
{
continue;
}
sum += distance;
count++;
}
}
return(sum / count);
}
/// <summary>
/// Subtract Operation
/// </summary>
/// <param name="result">ResultResampling Class</param>
/// <returns>ResultSpectrumCalculation</returns>
private SpectrumCalculationResult OperationSubtract(ResamplingResult result)
{
if (!ValidateResult(result))
{
return(null);
}
SpectrumCalculationResult spectrumResult = new SpectrumCalculationResult();
ClrDataPoints basePts = result.GetResultData(0);
List <ClrDataPoints> subtract = new List <ClrDataPoints>();
for (int i = 1; i < result.GetXYDataNum(); i++)
{
ClrDataPoints temp = new ClrDataPoints();
for (uint j = 0; j < basePts.getLength(); j++)
{
if (_stopFlag == true)
{
return(null);
}
temp.addPoint(basePts.getX(j),
result.GetResultData(i).getY(j) - basePts.getY(j));
}
subtract.Add(temp);
}
for (int i = 0; i < subtract.Count; i++)
{
if (_stopFlag == true)
{
return(null);
}
spectrumResult.AddResult(subtract[i], _specList[i + 1], SPECTRUMNAME_SUBTRACTED);
}
return(spectrumResult);
}
/// <summary>
/// Create Same array that first spectrum difference.
/// </summary>
/// <returns></returns>
private double[] CreateSameArrayFirstSpectrumDifference()
{
ClrDataPoints xydata = _param.GetXYData(0);
if (xydata == null)
{
return(null);
}
uint length = xydata.getLength();
uint count = 0;
double lower = GetLowerOutputRange();
double higher = GetHigherOutputRange();
for (uint i = 0; i < length; i++)
{
if ((xydata.getX(i) < lower) || (higher < xydata.getX(i)))
{
continue;
}
if (i == 0)
{
count++;
}
else if (xydata.getX(i) != xydata.getX(i - 1))
{
count++;
}
}
if (count == 0)
{
return(null);
}
double[] result = new double[count];
uint index = 0;
for (uint i = 0; i < length; i++)
{
if ((xydata.getX(i) < lower) || (higher < xydata.getX(i)))
{
continue;
}
if ((xydata.getX(i) == 0) ||
!result.Contains(xydata.getX(i)))
{
result[index++] = xydata.getX(i);
}
}
return(result);
}
/// <summary>
/// Gets the interval minimum of all spectrums.
/// </summary>
/// <returns>Interval</returns>
private double GetMinimumInterval()
{
double result = double.MaxValue;
for (int i = 0; i < _param.GetXYDataNum(); i++)
{
ClrDataPoints xydata = _param.GetXYData(i);
uint length = xydata.getLength();
for (uint j = 1; j < length; j++)
{
double distance = Math.Abs(xydata.getX(j) - xydata.getX(j - 1));
if (distance == 0)
{
continue;
}
result = Math.Min(distance, result);
}
}
return(result);
}
/// <summary>
/// Divide Operation
/// </summary>
/// <param name="result">ResultResampling Class</param>
/// <returns>ResultSpectrumCalculation</returns>
private SpectrumCalculationResult OperationDivide(ResamplingResult result)
{
if (!ValidateResult(result))
{
return(null);
}
SpectrumCalculationResult spectrumResult = new SpectrumCalculationResult();
ClrDataPoints basePts = new ClrDataPoints();
ClrDataPoints firstPts = result.GetResultData(0);
double threshold = firstPts.getMaxY() * Math.Pow(10, -6);
for (uint i = 0; i < firstPts.getLength(); i++)
{
if (_stopFlag == true)
{
return(null);
}
double value = Math.Max(firstPts.getY(i), threshold);
basePts.addPoint(firstPts.getX(i), value);
}
List <ClrDataPoints> subtract = new List <ClrDataPoints>();
for (int i = 1; i < result.GetXYDataNum(); i++)
{
ClrDataPoints temp = new ClrDataPoints();
for (uint j = 0; j < basePts.getLength(); j++)
{
if (_stopFlag == true)
{
return(null);
}
temp.addPoint(basePts.getX(j),
result.GetResultData(i).getY(j) / basePts.getY(j));
}
subtract.Add(temp);
}
//2013/11/26 - del
//spectrumResult.AddResult(basePts, _specList[0], SPECTRUMNAME_DIVIDED);
//enddel
for (int i = 0; i < subtract.Count; i++)
{
if (_stopFlag == true)
{
return(null);
}
spectrumResult.AddResult(subtract[i], _specList[i + 1], SPECTRUMNAME_DIVIDED);
}
return(spectrumResult);
}
/// <summary>
/// Calculate Sum of Data Points
/// </summary>
/// <param name="result">ResultResampling Class</param>
/// <returns>ClrDataPoints</returns>
private ClrDataPoints CalculateDataPointsSum(ResamplingResult result)
{
ClrDataPoints sum = result.GetResultData(0);
ClrDataPoints temp;
for (int i = 1; i < result.GetXYDataNum(); i++)
{
temp = sum;
sum = new ClrDataPoints();
ClrDataPoints data = result.GetResultData(i);
for (uint j = 0; j < data.getLength(); j++)
{
if (_stopFlag == true)
{
return(null);
}
sum.addPoint(data.getX(j), data.getY(j) + temp.getY(j));
}
}
return(sum);
}
/// <summary>
/// Average Operation
/// </summary>
/// <param name="result">ResultResampling Class</param>
/// <returns>ResultSpectrumCalculation</returns>
private SpectrumCalculationResult OperationAverage(ResamplingResult result)
{
if (!ValidateResult(result))
{
return(null);
}
SpectrumCalculationResult spectrumResult = new SpectrumCalculationResult();
ClrDataPoints sum = CalculateDataPointsSum(result);
ClrDataPoints average = new ClrDataPoints();
for (uint i = 0; i < sum.getLength(); i++)
{
if (_stopFlag == true)
{
return(null);
}
average.addPoint(
sum.getX(i),
sum.getY(i) / result.GetXYDataNum());
}
spectrumResult.AddResult(average, _specList[0], SPECTRUMNAME_AVERAGED);
return(spectrumResult);
}
private bool CreateBaselineSubtractedXIC(
PluginFunctionItemWrapper pfiw,
List <ClrDataPoints> resamplingList,
List <SpectrumWrapper> ms1List,
SettingParameterValuesWrapper spvw,
ref ClrDataPoints[] subtractLowerXICList,
ref ClrDataPoints[] subtractHigherXICList,
ref ClrDataPoints subtractHighestXICList
)
{
uint resamplingLength = resamplingList[0].getLength();
int lowerIndex = (resamplingLength < int.MaxValue) ? (int)resamplingLength : int.MaxValue;
int higherIndex = (0 < (int)(resamplingLength - lowerIndex))? (int)(resamplingLength - lowerIndex) : 0;
subtractLowerXICList = new ClrDataPoints[lowerIndex];
subtractHigherXICList = new ClrDataPoints[higherIndex];
for (uint i = 0; i < resamplingLength; i++)
{
//Update message.
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.REMOVE_CONTAMINANT_PEAK,
(int)i, (int)resamplingLength);
}
//Cancel.
if (StopFlag)
{
break;
}
//Create XIC.
ClrDataPoints pts = new ClrDataPoints();
for (int j = 0; j < resamplingList.Count; j++)
{
//Cancel.
if (StopFlag)
{
break;
}
pts.addPoint(ms1List[j].getRt(), resamplingList[j].getY(i));
}
//Cancel.
if (StopFlag)
{
pts.clearPoints();
pts.Dispose();
break;
}
//Baseline Subtraction
ClrParameters param = new ClrParameters();
ClrDataPoints baseline = new ClrDataPoints();
ClrPluginCallTool.setXYData(param, pts);
ClrPluginCallTool.setBaseline(param, baseline);
ClrPluginCallTool.setSettingValues(param, spvw);
pfiw.getCall().invoke(param);
//Cancel.
if (StopFlag)
{
param.Dispose();
baseline.clearPoints();
baseline.Dispose();
}
//Resampling baseline.
ClrDataPoints subtracted = new ClrDataPoints();
ResamplingParameter resamplingParam = new ResamplingParameter();
ResamplingCalculation resamplingCalc = new ResamplingCalculation(resamplingParam);
resamplingParam.ResamplingMode = ResamplingParameter.SamplingMode.FIRST;
resamplingParam.Interpolation = _resamplingParam.Interpolation;
resamplingParam.AddXYData(pts);
resamplingParam.AddXYData(baseline);
resamplingCalc.Execute();
ClrDataPoints resampledBaseline = resamplingCalc.Result.getResultData(1);
for (uint j = 0; j < resampledBaseline.getLength(); j++)
{
double intensity = Math.Max(pts.getY(j) - resampledBaseline.getY(j), 0);
subtracted.addPoint(pts.getX(j), intensity);
}
// Countermeasure to OutOfBoundsException.
if (i < int.MaxValue)
{
subtractLowerXICList[i] = subtracted;
}
else if (int.MaxValue < i && i < (uint)int.MaxValue * 2)
{
subtractHigherXICList[i - int.MaxValue] = subtracted;
}
else
{
subtractHighestXICList = subtracted;
}
resamplingParam.ClearXYDataList();
resamplingCalc.Result.ClearXYDataList();
}
return(!StopFlag);
}
/// <summary>
/// add xySetData to XYDataWrapper class
/// add data that set before calling this method to XYDataWrapper class
/// between min and max
/// </summary>
/// <param name="xyData">add to class</param>
/// <param name="minX">min(if this argument is below 0,min is not checked)</param>
/// <param name="maxX">max(if this argument is below 0,max is not checked)</param>
public override void onGetXYData(XYDataWrapper xyData, double minX, double maxX)
{
uint num;
if (_pts == null)
{
return;
}
xyData.clearPoints();
num = _pts.getLength();
xyData.reserve(num);
for (uint n = 0; n < num; n++)
{
if (((minX < 0) || (minX <= _pts.getX(n))) && ((maxX < 0) || (_pts.getX(n) <= maxX)))
{
xyData.addPoint(_pts.getX(n), _pts.getY(n));
}
}
}
