/// <summary>
/// Compile a 2D list of files organized by sample group for rMFE filtering
/// This list has input and output file paths (.rmc)
/// </summary>
/// <returns></returns>
private ICollection <ICollection <CompoundFilterByBucket.DataPathInfo> > GetFilePaths()
{
// outer list is by sample group
var rv = new List <ICollection <CompoundFilterByBucket.DataPathInfo> >();
foreach (var group in m_sampleGroupDict.Values.Distinct())
{
// inner list is by .rmc file
var grpList = new List <CompoundFilterByBucket.DataPathInfo>();
foreach (var file in m_sampleGroupDict.Where(sg => sg.Value == group).Select(sg => sg.Key))
{
// there can be multiple .unfiltered.rmc files depending on frag voltage, polarity, etc.
var rmcPath = FindCpdsMassHunter.GetPersistenceFilePath(file, null);
foreach (var rmcFile in Directory.GetFiles(rmcPath, "*" + RMC_UNFILTERED_EXTENSION))
{
var dpi = new CompoundFilterByBucket.DataPathInfo();
dpi.CustomerScalingFactor = 1.0f;
dpi.InputCompoundFilePath = rmcFile;
dpi.OutputCompoundFilePah = Regex.Replace(rmcFile, RMC_UNFILTERED_EXTENSION, RMC_EXTENSION);
grpList.Add(dpi);
}
}
rv.Add(grpList);
}
return(rv);
}
/// <summary>
/// Override to do the actual work of the command
/// </summary>
protected override void DoSpecialized()
{
//BatchExtractor.CommonUtility.LogMessage("Recursive MFE", this);
var userParameters = GetAlignmentParameters();
clcfileList.Clear();
if (IsGCData() == true) // To do recursive MFE for GC data
{
return;
}
//var progressTracker = new PFEProgressTracker(m_AppManager, ProgressCategory.Task);
try
{
//progressTracker.ReportProgress(ProgressStage.Starting, 0, new QualUserMessage(QualMessage.ExecutingFindCompounds));
for (int i = 0; i < m_analyses.Count; i++)
{
var m_analysis = m_analyses[i];
IFindCompoundsParameters findParams = GetFindCompoundsParams();
GetAnalysisSpecificParams(ref findParams, new object[] { m_analysis });
List <IonPolarity> polarityList = GetScanIonPolarities(findParams.DataAccess);
// for Allion data, not to use fragVoltage.
List <double> energyVoltages = null;
double lowE = double.NaN;
double[] highEs = null;
bool bMultipleCEs = false;
bool AllIonsData = FindCpdsUtilities.IsThisAllIonsData(findParams.DataAccess, out lowE, out highEs, out bMultipleCEs);
if (AllIonsData)
{
energyVoltages = new List <double>(1);
energyVoltages.Add(lowE);
}
else
{
energyVoltages = GetFragmentorVoltages(findParams.DataAccess);
if (energyVoltages.Count == 1)
{
energyVoltages[0] = 0.0;
}
}
// multiple time segemnt support. One segment per clc file.
// No MFE data segment with no clc file generated.
IBDADataAccess m_BdaDa = new BDADataAccess();
m_BdaDa.OpenDataFile(findParams.DataAccess.DataFileName, true);
IRange[] tempRange = m_BdaDa.GetTimeSegmentRanges();
int m_totalTimeSegment = tempRange.Length;
m_BdaDa.CloseDataFile();
//
double fragVoltage = 0.0;
// From B08, MFE data reader API has changed. It doesn't use the passed in multiple voltages. The reader handle it itself.
if (energyVoltages.Count > 1) // for multiple frag voltageas, we take the smallest one
{
// fragVoltage = energyVoltages.Min(); // match the changes in MassHunterAlgorithm.cs and in MFE (MFE agreed to do so)
}
DesiredMSStorageType storeType = DesiredMSStorageType.PeakElseProfile;
for (int idxPolarity = 0; idxPolarity < polarityList.Count; idxPolarity++)
{
IonPolarity ionPolarity = polarityList[idxPolarity];
foreach (var framVoltage in energyVoltages) // get one valid store type.
{
try
{
storeType = GetStorageType(findParams.DataAccess, ionPolarity, framVoltage);
break;
}
catch // small framVoltage different could get there, we use a valid one (TT 268031)
{
}
}
for (int segnum = 1; segnum <= m_totalTimeSegment; segnum++)
{
var sPath = FindCpdsMassHunter.GetPersistenceFilePath(
m_analysis.FilePath, null);
var sName = FindCpdsMassHunter.GetPersistenceFileName(
m_analysis.FilePath, ionPolarity, storeType, fragVoltage, segnum);
clcFileItem clcItem;
clcItem.rmcPath = Path.Combine(sPath, (sName + RMC_UNFILTERED_EXTENSION));
clcItem.clcPath = Path.Combine(sPath, (sName + CLC_EXTENSION));
clcItem.clcName = Regex.Replace(sName, @"^.+\.", String.Empty);
clcItem.scalingfactor = 1.0f;
clcfileList.Add(clcItem);
}
}
}
if (clcfileList.Count > 0)
{
var itemQuery = clcfileList.GroupBy(p => p.clcName);
string errMsg = string.Empty;
List <string> processedFilesList = new List <string>();
foreach (IGrouping <string, clcFileItem> queryItem in itemQuery)
{
List <string> clcFilePaths = new List <string> {
};
List <string> rmcFilePaths = new List <string> {
};
List <float> scalfactor = new List <float> {
};
foreach (var clcItem in queryItem)
{
if (File.Exists(clcItem.clcPath))
{
clcFilePaths.Add(clcItem.clcPath);
rmcFilePaths.Add(clcItem.rmcPath);
scalfactor.Add(clcItem.scalingfactor);
processedFilesList.Add(clcItem.clcPath);
}
}
if (clcFilePaths.Count > 0) // Do Recursive MFE only there is .clc file.
{
// Do RecursEngine
RecursiveMfeEngine recursMfeEng = new RecursiveMfeEngine(clcFilePaths, rmcFilePaths, scalfactor, userParameters);
for (int i = 0; i < recursMfeEng.StepCount; i++) // must start with 0.
{
//progressTracker.PercentComplete = (int)((double)(i+1) / recursMfeEng.StepCount * 100);
//progressTracker.ReportProgress(ProgressStage.Progressing, (int)((double)(i + 1) / recursMfeEng.StepCount * 100), "Refinding isotope cluster assignments...");
try
{
recursMfeEng.StepIt(i);
}
catch (Exception ex)
{
errMsg = ex.Message;
}
if (this.CancelCommandIndicator.Cancel == true)
{
throw new Exception("This operation was canceled.");
}
}
}
}
if (!string.IsNullOrEmpty(errMsg))
{
bool bOK = false;
foreach (string sF in processedFilesList)
{
string rmcFile = sF.Replace(".clc", ".rmc"); // if has rmc file be generated, at lease one of the time segment has data.
if (File.Exists(rmcFile))
{
bOK = true;
break;
}
}
if (!bOK)
{
throw new Exception(errMsg);
}
}
}
}
catch (Exception ex)
{
// IUserMessage msg = new UserMessage(0, string.Empty,
// ProgramModule.CoreDbSearch,
// ProgramModule.MfeEngine);
// throw new MSDAApplicationException(msg);
//throw new Exception("CmdPFRecursiveMFECpd : " + ex.Message);
var umsg = new QualUserMessage(QualMessage.MultipleAnalysisErrors_0, ex.Message);
throw new MSDAApplicationException(umsg);
}
finally
{
//progressTracker.ReportProgress(ProgressStage.Finished, 100, new QualUserMessage(QualMessage.OperationComplete));
Trace.WriteLineIf(Ts.TraceInfo, Tm.Finish);
}
}