/// <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>
/// Create Remove Contaminant Peak Result.
/// </summary>
/// <param name="scanNumbers">Scan Numbers</param>
/// <param name="tempDir">Temporal Directory</param>
/// <param name="ms1List">MS1 List</param>
/// <returns>Remove Contaminant Peak Result</returns>
private RemoveResult CreateRemoveResult(
int scanNumbers, string tempDir,
List <SpectrumWrapper> ms1List)
{
RemoveResult result = new RemoveResult();
for (int i = 0; i < scanNumbers; i++)
{
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.READ_FROM_TEMPORARY,
i, scanNumbers);
}
using (StreamReader sr = new StreamReader(tempDir + @"\Scan" + i.ToString() + ".csv"))
{
ClrDataPoints pts = new ClrDataPoints();
while (!sr.EndOfStream)
{
string[] splitLine = sr.ReadLine().Split(',');
double x = double.Parse(splitLine[0]);
double y = double.Parse(splitLine[1]);
pts.addPoint(x, y);
}
result.AddResult(pts, ms1List[i]);
}
}
return(result);
}
/// <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>
/// Add result data points(added data is clone).
/// </summary>
/// <param name="points"></param>
public void AddResult(ClrDataPoints points, SpectrumWrapper baseSpectrum, string name)
{
SpectrumResampling spectrum = new SpectrumResampling(baseSpectrum.getSample(), name);
spectrum.SetData(points);
_list.Add(spectrum);
}
/// <summary>
/// Execute Resampling.
/// </summary>
public void Execute()
{
Progress = 0;
if (_param == null)
{
return;
}
if (_result != null)
{
_result.Dispose();
}
_result = new ResamplingResult();
//Calculate resampling point.
double[] xi = CreateResamplingPoint();
if (xi == null)
{
return;
}
for (int i = 0; i < _param.GetXYDataNum(); i++)
{
if (StopFlag)
{
return;
}
ClrDataPoints xyData = _param.GetXYData(i);
double[] yi;
double[,] data;
yi = new double[xi.Length];
ConvertXYDataToXYArray(xyData, out data);
InterpolateMethod method = _param.Interpolation ==
ResamplingParameter.InterpolationAlgorithm.LINEAR ?
InterpolateMethod.LINEAR : InterpolateMethod.PCHIP;
if (UpdateResamplingProgress != null)
{
UpdateResamplingProgress(PROGRESS_RESAMPLING_PHASE.RESAMPLING_START, 0, i + 1, _param.GetXYDataNum());
}
WrapMatlabInterp1(yi, data.GetLength(1), data, xi.Length, xi, method, ExtrapolateType.FILL_ZERO);
_result.AddData(xi, yi);
if (UpdateResamplingProgress != null)
{
UpdateResamplingProgress(PROGRESS_RESAMPLING_PHASE.RESAMPLING_DOING, 0, i + 1, _param.GetXYDataNum());
}
Progress++;
}
if (UpdateResamplingProgress != null)
{
UpdateResamplingProgress(PROGRESS_RESAMPLING_PHASE.RESAMPLING_END, 0, _param.GetXYDataNum(), _param.GetXYDataNum());
}
}
/// <summary>
/// Submit latest result to sample tree.
/// </summary>
public void SubmitResultToTree()
{
// No Result
if (Result == null)
{
return;
}
ClrMsDataVariant msObj = new ClrMsDataVariant(_clrVariant);
DataGroupNodeWrapper dgnw = msObj.getSample().getRootDataGroupNode();
//Add result to sample tree.
SampleSetResampling sampleSet = new SampleSetResampling();
SampleResampling sample = new SampleResampling(sampleSet);
sample.openSample();
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
sample.setName("Contaminant peak removed " + msObj.getSample().getName());
root.setName("Contaminant peak removed " + dgnw.getName());
int cnt = 0;
for (int i = 0; i < Result.Spectrums.Count(); i++)
{
ClrDataPoints pts = Result.DataPoints[i];
SpectrumWrapper sw = Result.Spectrums[i];
XYDataWrapper xyd;
SpectrumResampling spec;
if (Result.Spectrums.Count == 1)
{
spec = new SpectrumResampling(sample, sw.getName());
}
else
{
cnt++;
spec = new SpectrumResampling(sample, Result.Spectrums[i].getName() + " (" + cnt.ToString() + ")");
}
xyd = spec.getXYData();
spec.SetData(pts);
spec.onGetXYData(xyd, -1.0, -1.0);
spec.setMinX(pts.getMinX());
spec.setMaxX(pts.getMaxX());
spec.setMaxIntensity(pts.getMaxY());
spec.setMsStage((int)sw.getMsStage());
sample.setSampleIndex((int)0);
root.addSpectrum(spec);
}
sampleSet.addSample(sample);
ClrPluginCallTool.onOpenSample(sample);
}
/// <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>
/// 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>
/// Set XYData To Resampling Calculation Class
/// </summary>
private void SetXYDataToResamplingCalculation()
{
_param.ClearXYDataList();
foreach (SpectrumWrapper spec in _specList)
{
if (_stopFlag == true)
{
break;
}
ClrDataPoints pts = new ClrDataPoints();
spec.getXYData(pts, false);
_param.AddXYData(pts);
}
}
/// <summary>
/// Display Calculation Results on tree view
/// </summary>
public void DisplayCalculationResult()
{
// No Result
if (_resultSpecCal == null)
{
return;
}
//Add result to sample tree.
SampleSetResampling sampleSet = new SampleSetResampling();
SampleResampling sample = new SampleResampling(sampleSet);
sample.openSample();
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
sample.setName(_resultSpecCal.Spectrums[0].getName() + " Sample");
root.setName(_resultSpecCal.Spectrums[0].getName() + " Sample");
int cnt = 0;
foreach (SpectrumResampling sr in _resultSpecCal.Spectrums)
{
ClrDataPoints xyd = new ClrDataPoints();
SpectrumResampling spec;
if (_resultSpecCal.Spectrums.Count == 1)
{
spec = new SpectrumResampling(sample, sr.getName() + " Spectrum");
}
else
{
cnt++;
spec = new SpectrumResampling(sample, sr.getName() + " Spectrum_" + cnt.ToString());
}
ClrDataPoints pts = new ClrDataPoints();
sr.getXYData(pts, false);
spec.getXYData(xyd, false);
spec.SetData(pts);
spec.setMinX(pts.getMinX());
spec.setMaxX(pts.getMaxX());
spec.setMaxIntensity(pts.getMaxY());
spec.onGetXYData(xyd, -1.0, -1.0);
spec.setMsStage((int)sr.getMsStage());
sample.setSampleIndex((int)0);
root.addSpectrum(spec);
}
sampleSet.addSample(sample);
ClrPluginCallTool.onOpenSample(sample);
}
/// <summary>
/// Set Spectrum calculation result to active object.
/// </summary>
/// <param name="resultSpecCal">Spectrum calculation result</param>
private static void SetResultToActiveObject(SpectrumCalculationResult resultSpecCal)
{
// Preparing Output files.
SampleSetResampling sampleSet = new SampleSetResampling();
SampleResampling sample = new SampleResampling(sampleSet);
sample.openSample();
DataGroupNodeWrapper root = sample.getRootDataGroupNode();
// _resultSpecCal.Spectrums[0].getName() returns
// "Average" or "Summed" or "Subtracted" or "Divided".
sample.setName(resultSpecCal.Spectrums[0].getName() + " " + SAMPLE_STRING);
root.setName(resultSpecCal.Spectrums[0].getName() + " " + SAMPLE_STRING);
int cnt = 0;
foreach (SpectrumResampling sr in resultSpecCal.Spectrums)
{
ClrDataPoints xyd = new ClrDataPoints();
SpectrumResampling spec;
if (resultSpecCal.Spectrums.Count == 1)
{
spec = new SpectrumResampling(sample, sr.getName() + " " + SPECTRUM_STRING);
}
else
{
cnt++;
spec = new SpectrumResampling(sample, sr.getName() + " " + SPECTRUM_STRING + "_" + cnt.ToString());
}
ClrDataPoints pts = new ClrDataPoints();
sr.getXYData(pts, false);
spec.getXYData(xyd, false);
spec.SetData(pts);
spec.setMinX(pts.getMinX());
spec.setMaxX(pts.getMaxX());
spec.setMaxIntensity(pts.getMaxY());
spec.onGetXYData(xyd, -1.0, -1.0);
spec.setMsStage((int)sr.getMsStage());
sample.setSampleIndex((int)0);
root.addSpectrum(spec);
}
sampleSet.addSample(sample);
// -out
kome.clr.ActiveObjectsManagerWrapper aoMgr = kome.clr.ActiveObjectsManagerWrapper.getInstance();
aoMgr.setActiveSample(sample);
}
/// <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>
/// 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>
/// Clear ClrDataPoints.
/// </summary>
/// <param name="subtractLowerXICList">Subtracted Lower XIC List</param>
/// <param name="subtractHigherXICList">Subtracted Higher XIC List</param>
/// <param name="subtractHighestXICList">Subtracted Highest XIC List</param>
/// <param name="resamplingList">Resampling List</param>
/// <param name="spvw">SettingParameterValuesWrapper</param>
private void ClearClrDataPoints(
ClrDataPoints[] subtractLowerXICList,
ClrDataPoints[] subtractHigherXICList,
ClrDataPoints subtractHighestXICList,
List <ClrDataPoints> resamplingList,
SettingParameterValuesWrapper spvw
)
{
foreach (ClrDataPoints pts in subtractLowerXICList)
{
if (pts == null)
{
break;
}
pts.clearPoints();
pts.Dispose();
}
foreach (ClrDataPoints pts in subtractHigherXICList)
{
pts.clearPoints();
pts.Dispose();
}
foreach (ClrDataPoints pts in resamplingList)
{
pts.clearPoints();
pts.Dispose();
}
if (subtractHighestXICList != null)
{
subtractHighestXICList.clearPoints();
subtractHighestXICList.Dispose();
}
spvw.clear();
spvw.Dispose();
}
/// <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);
}
/// <summary>
/// add xyData to XYDataWrapper list and RT data list
/// x arrengement number and y arrengement number have to be same
/// </summary>
/// <param name="x">x data arrengement</param>
/// <param name="y">y data arrengement</param>
/// <returns>ture:success/false:fail</returns>
public bool AddData(double[] x, double[] y)
{
ClrDataPoints xyData = new ClrDataPoints();
// Resampling Results are same number
if (x.Length != y.Length)
{
return(false);
}
if (_xyDataList.Count > 0)
{
if (x.Length != _xyDataList[0].getLength())
{
return(false);
}
}
for (int n = 0; n < x.Length; n++)
{
xyData.addPoint(x[n], y[n]);
}
_xyDataList.Add(xyData);
return(true);
}
/// <summary>
/// Execute Remove Contaminant Peak.
/// </summary>
/// <exception cref="ArgumentException"></exception>
/// <exception cref="ArgumentNullException"></exception>
public void Execute()
{
//Update Message
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.PREPARE,
(int)0, (int)1);
}
//Create Temporary Folder.
string tempDir = CreateTempDir();
if (tempDir == null)
{
return;
}
//Initialize.
StopFlag = false;
Result = null;
ResultRemove result = new ResultRemove();
//Get root node
ClrMsDataVariant msObj = new ClrMsDataVariant(_clrVariant);
DataGroupNodeWrapper dgnw = msObj.getSample().getRootDataGroupNode();
//Get all MS1 Spectrums.
List <SpectrumWrapper> ms1List = new List <SpectrumWrapper>();
ReadSpectrum(dgnw, ref ms1List);
//If count of MS1 Spectrums is 0, quit remove contaminant peak.
if (ms1List.Count <= 0)
{
//Update Message
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.CANCELLED,
(int)1, (int)1);
}
msObj.Dispose();
return;
}
else
{
foreach (SpectrumWrapper sw in ms1List)
{
_resamplingParam.AddXYData(sw.getXYData());
}
}
//Get wrappers
SettingParameterValuesWrapper spvw = new SettingParameterValuesWrapper();
PluginFunctionItemWrapper pfiw = PluginManagerWrapper.getInstance().getFunctionItem(
FUNCTIONTYPE_BASELINE, _baselineParam.Algorithm, null);
//Convert parameters to string for SettingParameterValuesWrapper.
string paramString = _baselineParam.ABCWindowWidth.ToString() + ","
+ _baselineParam.NoiseFactor.ToString() + ","
+ _baselineParam.SmoothingWidth.ToString();
pfiw.getSettingsPage().setParameterString(spvw, paramString);
if (StopFlag)
{
_resamplingParam.ClearXYDataList();
return;
}
_resampling.UpdateResamplingProgress += UpdateSpecCalcResamplingProgress;
//Resampling.
_resampling.Execute();
if (StopFlag)
{
_resamplingParam.ClearXYDataList();
return;
}
List <ClrDataPoints> resamplingList = _resampling.Result.getAllResultData();
_resampling.UpdateResamplingProgress -= UpdateSpecCalcResamplingProgress;
//Dispose.
_resamplingParam.ClearXYDataList();
//if resampling result is empty, quit remove contaminant peak.
if (resamplingList.Count == 0)
{
_resampling.Result.Dispose();
return;
}
//Garbage collect.
GC.Collect();
// Countermeasure to OutOfBoundsException.
// Max of List and Array Index is "int".
// Max Index of XYDataPoints is bigger than maximum integer.
// Maximum uint = (Maximum int) * 2 + 1.
ClrDataPoints[] subtractLowerXICList = null;
ClrDataPoints[] subtractHigherXICList = null;
ClrDataPoints subtractHighestXICList = null;
bool complete = true;
// Create Baseline subtracted XIC.
if (CreateBaselineSubtractedXIC(
pfiw,
resamplingList,
ms1List,
spvw,
ref subtractLowerXICList,
ref subtractHigherXICList,
ref subtractHighestXICList))
{
//Create XIC Complete.
uint count = (uint)(subtractHighestXICList == null ? 0 : 1);
count += (uint)subtractLowerXICList.Length;
count += (uint)subtractHigherXICList.Length;
//Replace intensity of resampled spectrum
for (int i = 0; i < resamplingList.Count; i++)
{
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.WRITE_TO_TEMPORARY,
i, resamplingList.Count);
}
if (StopFlag)
{
complete = false;
break;
}
try
{
using (StreamWriter sw = new StreamWriter(tempDir + @"\Scan" + i.ToString() + ".csv"))
{
for (uint j = 0; j < subtractLowerXICList.Length; j++)
{
if (j <= int.MaxValue)
{
sw.WriteLine(resamplingList[i].getX(j).ToString() + ","
+ subtractLowerXICList[(int)j].getY((uint)i).ToString());
}
else if (j == uint.MaxValue)
{
sw.WriteLine(resamplingList[i].getX(j).ToString() + ","
+ subtractHighestXICList.getY((uint)i).ToString());
}
else
{
sw.WriteLine(resamplingList[i].getX(j).ToString() + ","
+ subtractHigherXICList[(int)(j - int.MaxValue)].getY((uint)i).ToString());
}
}
}
}
catch
{
complete = false;
break;
}
}
}
else
{
complete = false;
}
int scanNumbers = resamplingList.Count;
foreach (ClrDataPoints pts in subtractLowerXICList)
{
if (pts == null)
{
break;
}
pts.clearPoints();
pts.Dispose();
}
foreach (ClrDataPoints pts in subtractHigherXICList)
{
pts.clearPoints();
pts.Dispose();
}
if (complete == false)
{
return;
}
foreach (ClrDataPoints pts in resamplingList)
{
pts.Dispose();
}
if (subtractHighestXICList != null)
{
subtractHighestXICList.clearPoints();
subtractHighestXICList.Dispose();
}
spvw.clear();
spvw.Dispose();
//Garbage collect.
GC.Collect();
if (StopFlag || !complete)
{
return;
}
for (int i = 0; i < scanNumbers; i++)
{
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.READ_FROM_TEMPORARY,
i, scanNumbers);
}
using (StreamReader sr = new StreamReader(tempDir + @"\Scan" + i.ToString() + ".csv"))
{
ClrDataPoints pts = new ClrDataPoints();
while (!sr.EndOfStream)
{
string[] splitLine = sr.ReadLine().Split(',');
double x = double.Parse(splitLine[0]);
double y = double.Parse(splitLine[1]);
pts.addPoint(x, y);
}
result.AddResult(pts, ms1List[i]);
}
}
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.COMPLETE,
1, 1);
}
Result = result;
GC.Collect();
return;
}
/// <summary>
/// add xyData to XYDataWrapper list
/// </summary>
/// <param name="xyData">XYDataWrapper</param>
public void AddXYData(ClrDataPoints xyData)
{
_xyDataList.Add(xyData);
}
/// <summary>
/// Create Temporal XIC Files.
/// </summary>
/// <param name="subtractLowerXICList">Subtracted Lower XIC List</param>
/// <param name="subtractHigherXICList">Subtracted Higher XIC List</param>
/// <param name="subtractHighestXICList">Subtracted Highest XIC List</param>
/// <param name="resamplingList">Resampling List</param>
/// <param name="tempDir">Temporal Directory</param>
/// <returns>Result</returns>
private bool CreateTempXICFiles(
ClrDataPoints[] subtractLowerXICList,
ClrDataPoints[] subtractHigherXICList,
ClrDataPoints subtractHighestXICList,
List <ClrDataPoints> resamplingList,
string tempDir)
{
uint count = (uint)(subtractHighestXICList == null ? 0 : 1);
count += (uint)subtractLowerXICList.Length;
count += (uint)subtractHigherXICList.Length;
//Replace intensity of resampled spectrum
for (int i = 0; i < resamplingList.Count; i++)
{
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.WRITE_TO_TEMPORARY,
i, resamplingList.Count);
}
if (StopFlag)
{
return(false);
}
try
{
using (StreamWriter sw = new StreamWriter(tempDir + @"\Scan" + i.ToString() + ".csv"))
{
for (uint j = 0; j < count; j++)
{
int xicIndex = 0;
double x = resamplingList[i].getX(j);
if (x < _resamplingParam.OutputLowerRange || _resamplingParam.OutputHigherRange < x)
{
continue;
}
if (j <= int.MaxValue)
{
sw.WriteLine(x.ToString() + "," + subtractLowerXICList[(int)j].getY((uint)xicIndex).ToString());
}
else if (j == uint.MaxValue)
{
sw.WriteLine(x + "," + subtractHighestXICList.getY((uint)xicIndex).ToString());
}
else
{
sw.WriteLine(x + "," + subtractHigherXICList[(int)(j - int.MaxValue)].getY((uint)xicIndex).ToString());
}
xicIndex++;
}
}
}
catch
{
return(false);
}
}
return(true);
}
/// <summary>
/// Execute Remove Contaminant Peak.
/// </summary>
/// <exception cref="ArgumentException"></exception>
/// <exception cref="ArgumentNullException"></exception>
public void Execute()
{
//Update Message
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.PREPARE,
(int)0, (int)1);
}
//Create Temporary Folder.
string tempDir = CreateTempDir();
if (tempDir == null)
{
return;
}
//Initialize.
StopFlag = false;
if (Result != null)
{
Result.ClearResult();
}
Result = null;
//Get root node
ClrMsDataVariant msObj = new ClrMsDataVariant(_clrVariant);
DataGroupNodeWrapper dgnw = msObj.getSample().getRootDataGroupNode();
//Get all MS1 Spectrums.
List <SpectrumWrapper> ms1List = new List <SpectrumWrapper>();
ReadSpectrum(dgnw, ref ms1List);
//If count of MS1 Spectrums is 0, quit remove contaminant peak.
if (ms1List.Count <= 0)
{
//Update Message
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.CANCELED, 1, 1);
}
msObj.Dispose();
return;
}
//Create Resampling parameters.
foreach (SpectrumWrapper sw in ms1List)
{
ClrDataPoints pts = new ClrDataPoints();
sw.getXYData(pts, false);
_resamplingParam.AddXYData(pts);
}
//Get wrappers
SettingParameterValuesWrapper spvw = new SettingParameterValuesWrapper();
PluginFunctionItemWrapper pfiw = PluginManagerWrapper.getInstance().getFunctionItem(
FUNCTIONTYPE_BASELINE, _baselineParam.Algorithm, null);
//Convert parameters to string for SettingParameterValuesWrapper.
string paramString = _baselineParam.ABCWindowWidth.ToString() + ","
+ _baselineParam.NoiseFactor.ToString() + ","
+ _baselineParam.SmoothingWidth.ToString();
pfiw.getSettingsPage().setParameterString(spvw, paramString);
if (StopFlag)
{
_resamplingParam.ClearXYDataList();
return;
}
_resampling.UpdateResamplingProgress += UpdateSpecCalcResamplingProgress;
//Resampling.
_resampling.Execute();
if (StopFlag)
{
_resamplingParam.ClearXYDataList();
return;
}
List <ClrDataPoints> resamplingList = _resampling.Result.GetAllResultData();
_resampling.UpdateResamplingProgress -= UpdateSpecCalcResamplingProgress;
//Dispose.
_resamplingParam.ClearXYDataList();
//if resampling result is empty, quit remove contaminant peak.
if (resamplingList.Count == 0)
{
_resampling.Result.Dispose();
return;
}
// Countermeasure to OutOfBoundsException.
// Max of List and Array Index is "int".
// Max Index of XYDataPoints is bigger than maximum integer.
// Maximum uint = (Maximum int) * 2 + 1.
ClrDataPoints[] subtractLowerXICList = null;
ClrDataPoints[] subtractHigherXICList = null;
ClrDataPoints subtractHighestXICList = null;
bool complete = true;
// Create Baseline subtracted XIC.
if (CreateBaselineSubtractedXIC(
pfiw, resamplingList, ms1List, spvw,
ref subtractLowerXICList,
ref subtractHigherXICList,
ref subtractHighestXICList))
{
complete = CreateTempXICFiles(subtractLowerXICList,
subtractHigherXICList, subtractHighestXICList,
resamplingList, tempDir);
}
else
{
complete = false;
}
int scanNumbers = resamplingList.Count;
ClearClrDataPoints(
subtractLowerXICList,
subtractHigherXICList,
subtractHighestXICList,
resamplingList, spvw);
if (StopFlag || !complete)
{
return;
}
if (UpdateProgress != null)
{
UpdateProgress(
PROGRESS_REMOVECONTAMINANT_PHASE.COMPLETE,
1, 1);
}
Result = CreateRemoveResult(scanNumbers, tempDir, ms1List);
return;
}
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 result data points.
/// </summary>
/// <param name="points"></param>
public void AddResult(ClrDataPoints points, SpectrumWrapper baseSpectrum)
{
_ptsList.Add(points);
_specList.Add(baseSpectrum);
}
/// <summary>
/// set Datapoints for onGetXYData
/// </summary>
/// <param name="pts">ClrDataPoints</param>
public void SetData(ClrDataPoints pts)
{
_pts = pts;
}
