/// <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>
/// 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;
}
