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SICProcessing.cs
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SICProcessing.cs
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using System;
using System.Collections.Generic;
using System.Linq;
using MASIC.Data;
using MASIC.DataOutput;
using MASIC.Options;
using MASICPeakFinder;
namespace MASIC
{
/// <summary>
/// This class creates selected ion chromatograms for parent ions
/// </summary>
public class SICProcessing : MasicEventNotifier
{
// Ignore Spelling: MASIC, mrm
private const string CREATING_SICS = "Creating SIC's for parent ions";
private readonly clsMASICPeakFinder mMASICPeakFinder;
private readonly MRMProcessing mMRMProcessor;
/// <summary>
/// Constructor
/// </summary>
public SICProcessing(clsMASICPeakFinder peakFinder, MRMProcessing mrmProcessor)
{
mMASICPeakFinder = peakFinder;
mMRMProcessor = mrmProcessor;
}
private static short ComputeMzSearchChunkProgress(
int parentIonsProcessed, int parentIonsCount,
int surveyScanIndex, int surveyScansCount,
double mzSearchChunkProgressFraction)
{
var progressAddon = surveyScanIndex / (double)surveyScansCount * mzSearchChunkProgressFraction * 100;
if (parentIonsCount < 1)
{
return (short)Math.Round(progressAddon, 0);
}
var percentComplete = parentIonsProcessed / (double)(parentIonsCount - 1) * 100 + progressAddon;
return (short)Math.Round(percentComplete, 0);
}
private static List<MzBinInfo> CreateMZLookupList(
MASICOptions masicOptions,
ScanList scanList,
bool processSIMScans,
int simIndex)
{
var mzBinList = new List<MzBinInfo>(scanList.ParentIons.Count);
var sicOptions = masicOptions.SICOptions;
for (var parentIonIndex = 0; parentIonIndex < scanList.ParentIons.Count; parentIonIndex++)
{
bool includeParentIon;
if (scanList.ParentIons[parentIonIndex].IsDIA)
{
includeParentIon = false;
}
else if (scanList.ParentIons[parentIonIndex].MRMDaughterMZ > 0)
{
includeParentIon = false;
}
else if (masicOptions.CustomSICList.LimitSearchToCustomMZList)
{
// Always include CustomSICPeak entries
includeParentIon = scanList.ParentIons[parentIonIndex].CustomSICPeak;
}
else
{
// Use processingSIMScans and .SIMScan to decide whether to include the entry
var surveyScan = scanList.SurveyScans[scanList.ParentIons[parentIonIndex].SurveyScanIndex];
if (processSIMScans)
{
if (surveyScan.SIMScan)
{
includeParentIon = surveyScan.SIMIndex == simIndex;
}
else
{
includeParentIon = false;
}
}
else
{
includeParentIon = !surveyScan.SIMScan;
}
}
if (!includeParentIon)
{
continue;
}
var newMzBin = new MzBinInfo
{
MZ = scanList.ParentIons[parentIonIndex].MZ,
ParentIonIndex = parentIonIndex
};
if (scanList.ParentIons[parentIonIndex].CustomSICPeak)
{
newMzBin.MZTolerance = scanList.ParentIons[parentIonIndex].CustomSICPeakMZToleranceDa;
newMzBin.MZToleranceIsPPM = false;
}
else
{
newMzBin.MZTolerance = sicOptions.SICTolerance;
newMzBin.MZToleranceIsPPM = sicOptions.SICToleranceIsPPM;
}
mzBinList.Add(newMzBin);
}
// Sort mzBinList by m/z
return mzBinList.OrderBy(item => item.MZ).ToList();
}
/// <summary>
/// Create selected ion chromatograms for the parent ions
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="masicOptions"></param>
/// <param name="dataOutputHandler"></param>
/// <param name="sicProcessor"></param>
/// <param name="xmlResultsWriter"></param>
public bool CreateParentIonSICs(
ScanList scanList,
SpectraCache spectraCache,
MASICOptions masicOptions,
DataOutput.DataOutput dataOutputHandler,
SICProcessing sicProcessor,
XMLResultsWriter xmlResultsWriter)
{
var success = false;
if (scanList.ParentIons.Count == 0)
{
// No parent ions
if (masicOptions.SuppressNoParentIonsError)
{
return true;
}
SetLocalErrorCode(clsMASIC.MasicErrorCodes.NoParentIonsFoundInInputFile);
return false;
}
if (scanList.SurveyScans.Count == 0)
{
// No survey scans
if (masicOptions.SuppressNoParentIonsError)
{
return true;
}
SetLocalErrorCode(clsMASIC.MasicErrorCodes.NoSurveyScansFoundInInputFile);
return false;
}
try
{
var parentIonsProcessed = 0;
masicOptions.LastParentIonProcessingLogTime = DateTime.UtcNow;
UpdateProgress(0, CREATING_SICS);
Console.Write(CREATING_SICS);
ReportMessage(CREATING_SICS);
// Create an array of m/z values in scanList.ParentIons, sort by m/z
// Next, step through the data in order of m/z, creating SICs for each grouping of m/z's within half of the SIC tolerance
// First process the non SIM, non MRM scans
// If this file only has MRM scans, CreateMZLookupList will return False
var mzBinList = CreateMZLookupList(masicOptions, scanList, false, 0);
if (mzBinList.Count > 0)
{
success = ProcessMZList(
scanList, spectraCache, masicOptions,
dataOutputHandler, xmlResultsWriter,
mzBinList, false, 0, ref parentIonsProcessed);
}
if (success && !masicOptions.CustomSICList.LimitSearchToCustomMZList)
{
// Now process the SIM scans (if any)
// First, see if any SIMScans are present and determine the maximum SIM Index
var simIndexMax = -1;
foreach (var parentIon in scanList.ParentIons)
{
var surveyScan = scanList.SurveyScans[parentIon.SurveyScanIndex];
if (surveyScan.SIMScan && surveyScan.SIMIndex > simIndexMax)
{
simIndexMax = surveyScan.SIMIndex;
}
}
// Now process each SIM Scan type
for (var simIndex = 0; simIndex <= simIndexMax; simIndex++)
{
var mzBinListSIM = CreateMZLookupList(masicOptions, scanList, true, simIndex);
if (mzBinListSIM.Count > 0)
{
ProcessMZList(
scanList, spectraCache, masicOptions,
dataOutputHandler, xmlResultsWriter,
mzBinListSIM, true, simIndex, ref parentIonsProcessed);
}
}
}
// Lastly, process the MRM scans (if any)
if (scanList.MRMDataPresent)
{
mMRMProcessor.ProcessMRMList(scanList, spectraCache, sicProcessor, xmlResultsWriter, mMASICPeakFinder, ref parentIonsProcessed);
}
Console.WriteLine();
return true;
}
catch (Exception ex)
{
ReportError("Error creating Parent Ion SICs", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
return false;
}
}
private SICStatsPeak ExtractSICDetailsFromFullSIC(
int mzIndexWork,
List<BaselineNoiseStatsSegment> baselineNoiseStatSegments,
int fullSICDataCount,
int[,] fullSICScanIndices,
double[,] fullSICIntensities,
double[,] fullSICMasses,
ScanList scanList,
int scanIndexObservedInFullSIC,
SICDetails sicDetails,
MASICOptions masicOptions,
ScanNumScanTimeConversion scanNumScanConverter,
bool customSICPeak,
float customSICPeakScanOrAcqTimeTolerance)
{
// Minimum number of scans to extend left or right of the scan that meets the minimum intensity threshold requirement
const int MINIMUM_NOISE_SCANS_TO_INCLUDE = 10;
float customSICScanToleranceMinutesHalfWidth = 0;
// Pointers to entries in fullSICScanIndices() and fullSICIntensities()
int scanIndexStart = 0, scanIndexEnd = 0;
var maximumIntensity = 0.0;
var sicOptions = masicOptions.SICOptions;
var baselineNoiseStats = mMASICPeakFinder.LookupNoiseStatsUsingSegments(scanIndexObservedInFullSIC, baselineNoiseStatSegments);
// Initialize the peak
var sicPeak = new SICStatsPeak
{
BaselineNoiseStats = baselineNoiseStats
};
// Initialize the values for the maximum width of the SIC peak; these might get altered for custom SIC values
var maxSICPeakWidthMinutesBackward = sicOptions.MaxSICPeakWidthMinutesBackward;
var maxSICPeakWidthMinutesForward = sicOptions.MaxSICPeakWidthMinutesForward;
// Limit the data examined to a portion of fullSICScanIndices() and fullSICIntensities, populating sicDetails
try
{
// Initialize customSICScanToleranceHalfWidth
if (customSICPeakScanOrAcqTimeTolerance < float.Epsilon)
{
customSICPeakScanOrAcqTimeTolerance = masicOptions.CustomSICList.ScanOrAcqTimeTolerance;
}
if (customSICPeakScanOrAcqTimeTolerance < float.Epsilon)
{
// Use the entire SIC
// Specify this by setting customSICScanToleranceMinutesHalfWidth to the maximum scan time in .MasterScanTimeList()
if (scanList.MasterScanOrderCount > 0)
{
customSICScanToleranceMinutesHalfWidth = scanList.MasterScanTimeList[scanList.MasterScanOrderCount - 1];
}
else
{
customSICScanToleranceMinutesHalfWidth = float.MaxValue;
}
}
else
{
if (masicOptions.CustomSICList.ScanToleranceType == CustomSICList.CustomSICScanTypeConstants.Relative && customSICPeakScanOrAcqTimeTolerance > 10)
{
// Relative scan time should only range from 0 to 1; we'll allow values up to 10
customSICPeakScanOrAcqTimeTolerance = 10;
}
customSICScanToleranceMinutesHalfWidth = scanNumScanConverter.ScanOrAcqTimeToScanTime(
scanList, customSICPeakScanOrAcqTimeTolerance / 2, masicOptions.CustomSICList.ScanToleranceType, true);
}
if (customSICPeak)
{
if (maxSICPeakWidthMinutesBackward < customSICScanToleranceMinutesHalfWidth)
{
maxSICPeakWidthMinutesBackward = customSICScanToleranceMinutesHalfWidth;
}
if (maxSICPeakWidthMinutesForward < customSICScanToleranceMinutesHalfWidth)
{
maxSICPeakWidthMinutesForward = customSICScanToleranceMinutesHalfWidth;
}
}
// Initially use just 3 survey scans, centered around scanIndexObservedInFullSIC
if (scanIndexObservedInFullSIC > 0)
{
scanIndexStart = scanIndexObservedInFullSIC - 1;
scanIndexEnd = scanIndexObservedInFullSIC + 1;
}
else
{
scanIndexStart = 0;
scanIndexEnd = 1;
scanIndexObservedInFullSIC = 0;
}
if (scanIndexEnd >= fullSICDataCount)
scanIndexEnd = fullSICDataCount - 1;
}
catch (Exception ex)
{
ReportError("Error initializing SIC start/end indices", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
if (scanIndexEnd >= scanIndexStart)
{
var scanIndexMax = 0;
try
{
// Start by using the 3 survey scans centered around scanIndexObservedInFullSIC
maximumIntensity = -1;
scanIndexMax = -1;
for (var scanIndex = scanIndexStart; scanIndex <= scanIndexEnd; scanIndex++)
{
if (fullSICIntensities[mzIndexWork, scanIndex] > maximumIntensity)
{
maximumIntensity = fullSICIntensities[mzIndexWork, scanIndex];
scanIndexMax = scanIndex;
}
}
}
catch (Exception ex)
{
ReportError("Error while creating initial SIC", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
// Now extend the SIC, stepping left and right until a threshold is reached
var leftDone = false;
var rightDone = false;
// The index of the first scan found to be below threshold (on the left)
var scanIndexBelowThresholdLeft = -1;
// The index of the first scan found to be below threshold (on the right)
var scanIndexBelowThresholdRight = -1;
while (scanIndexStart > 0 && !leftDone || scanIndexEnd < fullSICDataCount - 1 && !rightDone)
{
try
{
// Extend the SIC to the left until the threshold is reached
if (scanIndexStart > 0 && !leftDone)
{
if (fullSICIntensities[mzIndexWork, scanIndexStart] < sicOptions.SICPeakFinderOptions.IntensityThresholdAbsoluteMinimum ||
fullSICIntensities[mzIndexWork, scanIndexStart] < sicOptions.SICPeakFinderOptions.IntensityThresholdFractionMax * maximumIntensity ||
fullSICIntensities[mzIndexWork, scanIndexStart] < sicPeak.BaselineNoiseStats.NoiseLevel)
{
if (scanIndexBelowThresholdLeft < 0)
{
scanIndexBelowThresholdLeft = scanIndexStart;
}
else if (scanIndexStart <= scanIndexBelowThresholdLeft - MINIMUM_NOISE_SCANS_TO_INCLUDE)
{
// We have now processed MINIMUM_NOISE_SCANS_TO_INCLUDE+1 scans that are below the thresholds
// Stop creating the SIC to the left
leftDone = true;
}
}
else
{
scanIndexBelowThresholdLeft = -1;
}
var peakWidthMinutesBackward =
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexObservedInFullSIC]].ScanTime -
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexStart]].ScanTime;
if (leftDone)
{
// Require a minimum distance of InitialPeakWidthScansMaximum data points to the left of scanIndexObservedInFullSIC and to the left of scanIndexMax
if (scanIndexObservedInFullSIC - scanIndexStart < sicOptions.SICPeakFinderOptions.InitialPeakWidthScansMaximum)
leftDone = false;
if (scanIndexMax - scanIndexStart < sicOptions.SICPeakFinderOptions.InitialPeakWidthScansMaximum)
leftDone = false;
// For custom SIC values, make sure the scan range has been satisfied
if (leftDone && customSICPeak && peakWidthMinutesBackward < customSICScanToleranceMinutesHalfWidth)
{
leftDone = false;
}
}
if (!leftDone)
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (scanIndexStart == 0)
{
leftDone = true;
}
else
{
scanIndexStart--;
if (fullSICIntensities[mzIndexWork, scanIndexStart] > maximumIntensity)
{
maximumIntensity = fullSICIntensities[mzIndexWork, scanIndexStart];
scanIndexMax = scanIndexStart;
}
}
}
peakWidthMinutesBackward = scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexObservedInFullSIC]].ScanTime -
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexStart]].ScanTime;
if (peakWidthMinutesBackward >= maxSICPeakWidthMinutesBackward)
{
leftDone = true;
}
}
}
catch (Exception ex)
{
ReportError("Error extending SIC to the left", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
try
{
// Extend the SIC to the right until the threshold is reached
if (scanIndexEnd < fullSICDataCount - 1 && !rightDone)
{
if (fullSICIntensities[mzIndexWork, scanIndexEnd] < sicOptions.SICPeakFinderOptions.IntensityThresholdAbsoluteMinimum ||
fullSICIntensities[mzIndexWork, scanIndexEnd] < sicOptions.SICPeakFinderOptions.IntensityThresholdFractionMax * maximumIntensity ||
fullSICIntensities[mzIndexWork, scanIndexEnd] < sicPeak.BaselineNoiseStats.NoiseLevel)
{
if (scanIndexBelowThresholdRight < 0)
{
scanIndexBelowThresholdRight = scanIndexEnd;
}
else if (scanIndexEnd >= scanIndexBelowThresholdRight + MINIMUM_NOISE_SCANS_TO_INCLUDE)
{
// We have now processed MINIMUM_NOISE_SCANS_TO_INCLUDE+1 scans that are below the thresholds
// Stop creating the SIC to the right
rightDone = true;
}
}
else
{
scanIndexBelowThresholdRight = -1;
}
var peakWidthMinutesForward =
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexEnd]].ScanTime -
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexObservedInFullSIC]].ScanTime;
if (rightDone)
{
// Require a minimum distance of InitialPeakWidthScansMaximum data points to the right of scanIndexObservedInFullSIC and to the right of scanIndexMax
if (scanIndexEnd - scanIndexObservedInFullSIC < sicOptions.SICPeakFinderOptions.InitialPeakWidthScansMaximum)
rightDone = false;
if (scanIndexEnd - scanIndexMax < sicOptions.SICPeakFinderOptions.InitialPeakWidthScansMaximum)
rightDone = false;
// For custom SIC values, make sure the scan range has been satisfied
if (rightDone && customSICPeak && peakWidthMinutesForward < customSICScanToleranceMinutesHalfWidth)
{
rightDone = false;
}
}
if (!rightDone)
{
if (scanIndexEnd == fullSICDataCount - 1)
{
rightDone = true;
}
else
{
scanIndexEnd++;
if (fullSICIntensities[mzIndexWork, scanIndexEnd] > maximumIntensity)
{
maximumIntensity = fullSICIntensities[mzIndexWork, scanIndexEnd];
scanIndexMax = scanIndexEnd;
}
}
}
peakWidthMinutesForward = scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexEnd]].ScanTime -
scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndexObservedInFullSIC]].ScanTime;
if (peakWidthMinutesForward >= maxSICPeakWidthMinutesForward)
{
rightDone = true;
}
}
}
catch (Exception ex)
{
ReportError("Error extending SIC to the right", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
} // While Not LeftDone and Not RightDone
}
// Populate sicDetails with the data between scanIndexStart and scanIndexEnd
if (scanIndexStart < 0)
scanIndexStart = 0;
if (scanIndexEnd >= fullSICDataCount)
scanIndexEnd = fullSICDataCount - 1;
if (scanIndexEnd < scanIndexStart)
{
ReportError("Programming error: scanIndexEnd < scanIndexStart", clsMASIC.MasicErrorCodes.FindSICPeaksError);
scanIndexEnd = scanIndexStart;
}
try
{
// Copy the scan index values from fullSICScanIndices to .SICScanIndices()
// Copy the intensity values from fullSICIntensities() to .SICData()
// Copy the mz values from fullSICMasses() to .SICMasses()
sicDetails.SICScanType = ScanList.ScanTypeConstants.SurveyScan;
sicDetails.SICData.Clear();
sicPeak.IndexObserved = 0;
for (var scanIndex = scanIndexStart; scanIndex <= scanIndexEnd; scanIndex++)
{
if (fullSICScanIndices[mzIndexWork, scanIndex] >= 0)
{
sicDetails.AddData(scanList.SurveyScans[fullSICScanIndices[mzIndexWork, scanIndex]].ScanNumber,
fullSICIntensities[mzIndexWork, scanIndex],
fullSICMasses[mzIndexWork, scanIndex],
fullSICScanIndices[mzIndexWork, scanIndex]);
if (scanIndex == scanIndexObservedInFullSIC)
{
sicPeak.IndexObserved = sicDetails.SICDataCount - 1;
}
}
else
{
// This shouldn't happen
}
}
}
catch (Exception ex)
{
ReportError("Error populating .SICScanIndices, .SICData, and .SICMasses", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
return sicPeak;
}
private bool ProcessMZList(
ScanList scanList,
SpectraCache spectraCache,
MASICOptions masicOptions,
DataOutput.DataOutput dataOutputHandler,
XMLResultsWriter xmlResultsWriter,
IReadOnlyList<MzBinInfo> mzBinList,
bool processSIMScans,
int simIndex,
ref int parentIonsProcessed)
{
// Step through the data in order of m/z, creating SICs for each grouping of m/z's within half of the SIC tolerance
// Note that mzBinList and parentIonIndices() are parallel arrays, with mzBinList() sorted on ascending m/z
const int MAX_RAW_DATA_MEMORY_USAGE_MB = 50;
int maxMZCountInChunk;
var mzSearchChunks = new List<MzSearchInfo>(mzBinList.Count);
bool[] parentIonUpdated;
try
{
// Determine the maximum number of m/z values to process simultaneously
// Limit the total memory usage to ~50 MB
// Each m/z value will require 12 bytes per scan
if (scanList.SurveyScans.Count > 0)
{
maxMZCountInChunk = (int)(MAX_RAW_DATA_MEMORY_USAGE_MB * 1024 * 1024 / (double)(scanList.SurveyScans.Count * 12));
}
else
{
maxMZCountInChunk = 1;
}
if (maxMZCountInChunk > mzBinList.Count)
{
maxMZCountInChunk = mzBinList.Count;
}
if (maxMZCountInChunk < 1)
maxMZCountInChunk = 1;
// Reserve room in parentIonUpdated
parentIonUpdated = new bool[mzBinList.Count];
}
catch (Exception ex)
{
ReportError("Error reserving memory for the m/z chunks", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
return false;
}
try
{
var dataAggregation = new DataAggregation();
RegisterEvents(dataAggregation);
var scanNumScanConverter = new ScanNumScanTimeConversion();
RegisterEvents(scanNumScanConverter);
var parentIonIndices = (from item in mzBinList select item.ParentIonIndex).ToList();
for (var mzIndex = 0; mzIndex < mzBinList.Count; mzIndex++)
{
// ---------------------------------------------------------
// Find the next group of m/z values to use, starting with mzIndex
// ---------------------------------------------------------
// Initially set the MZIndexStart to mzIndex
// Look for adjacent m/z values within udtMZBinList(.MZIndexStart).MZToleranceDa / 2
// of the m/z value that starts this group
// Only group m/z values with the same udtMZBinList().MZTolerance and udtMZBinList().MZToleranceIsPPM values
var mzSearchChunk = new MzSearchInfo
{
MZIndexStart = mzIndex,
MZTolerance = mzBinList[mzIndex].MZTolerance,
MZToleranceIsPPM = mzBinList[mzIndex].MZToleranceIsPPM
};
double mzToleranceDa;
if (mzSearchChunk.MZToleranceIsPPM)
{
mzToleranceDa = Utilities.PPMToMass(mzSearchChunk.MZTolerance, mzBinList[mzSearchChunk.MZIndexStart].MZ);
}
else
{
mzToleranceDa = mzSearchChunk.MZTolerance;
}
while (mzIndex < mzBinList.Count - 2 &&
Math.Abs(mzBinList[mzIndex + 1].MZTolerance - mzSearchChunk.MZTolerance) < double.Epsilon &&
mzBinList[mzIndex + 1].MZToleranceIsPPM == mzSearchChunk.MZToleranceIsPPM &&
mzBinList[mzIndex + 1].MZ - mzBinList[mzSearchChunk.MZIndexStart].MZ <= mzToleranceDa / 2)
{
mzIndex++;
}
mzSearchChunk.MZIndexEnd = mzIndex;
if (mzSearchChunk.MZIndexEnd == mzSearchChunk.MZIndexStart)
{
mzSearchChunk.MZIndexMidpoint = mzSearchChunk.MZIndexEnd;
mzSearchChunk.SearchMZ = mzBinList[mzSearchChunk.MZIndexStart].MZ;
}
// Determine the median m/z of the members in the m/z group
else if ((mzSearchChunk.MZIndexEnd - mzSearchChunk.MZIndexStart) % 2 == 0)
{
// Odd number of points; use the m/z value of the midpoint
mzSearchChunk.MZIndexMidpoint = mzSearchChunk.MZIndexStart + (int)Math.Round((mzSearchChunk.MZIndexEnd - mzSearchChunk.MZIndexStart) / (double)2);
mzSearchChunk.SearchMZ = mzBinList[mzSearchChunk.MZIndexMidpoint].MZ;
}
else
{
// Even number of points; average the values on either side of (.mzIndexEnd - .mzIndexStart / 2)
mzSearchChunk.MZIndexMidpoint = mzSearchChunk.MZIndexStart + (int)Math.Floor((mzSearchChunk.MZIndexEnd - mzSearchChunk.MZIndexStart) / 2.0);
mzSearchChunk.SearchMZ = (mzBinList[mzSearchChunk.MZIndexMidpoint].MZ + mzBinList[mzSearchChunk.MZIndexMidpoint + 1].MZ) / 2;
}
mzSearchChunks.Add(mzSearchChunk);
if (mzSearchChunks.Count >= maxMZCountInChunk || mzIndex == mzBinList.Count - 1)
{
// ---------------------------------------------------------
// Reached maxMZCountInChunk m/z value
// Process all the m/z values in udtMZSearchChunk
// ---------------------------------------------------------
var mzSearchChunkProgressFraction = mzSearchChunks.Count / (double)mzBinList.Count;
var success = ProcessMzSearchChunk(
masicOptions,
scanList,
dataAggregation, dataOutputHandler, xmlResultsWriter,
spectraCache, scanNumScanConverter,
mzSearchChunks,
mzSearchChunkProgressFraction,
parentIonIndices,
processSIMScans,
simIndex,
parentIonUpdated,
ref parentIonsProcessed);
if (!success)
{
return false;
}
// Clear mzSearchChunks
mzSearchChunks.Clear();
}
if (masicOptions.AbortProcessing)
{
scanList.ProcessingIncomplete = true;
break;
}
}
return true;
}
catch (Exception ex)
{
ReportError("Error processing the m/z chunks to create the SIC data", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
return false;
}
}
private bool ProcessMzSearchChunk(
MASICOptions masicOptions,
ScanList scanList,
DataAggregation dataAggregation,
DataOutput.DataOutput dataOutputHandler,
XMLResultsWriter xmlResultsWriter,
SpectraCache spectraCache,
ScanNumScanTimeConversion scanNumScanConverter,
IReadOnlyList<MzSearchInfo> mzSearchChunk,
double mzSearchChunkProgressFraction,
IList<int> parentIonIndices,
bool processSIMScans,
int simIndex,
IList<bool> parentIonUpdated,
ref int parentIonsProcessed)
{
// The following are 2D arrays, ranging from 0 to mzSearchChunkCount-1 in the first dimension and 0 to .SurveyScans.Count - 1 in the second dimension
// We could have included these in udtMZSearchChunk but memory management is more efficient if I use 2D arrays for this data
// Reserve room in fullSICScanIndices for at most maxMZCountInChunk values and .SurveyScans.Count scans
// Count of the number of valid entries in the second dimension of the above 3 arrays
var fullSICDataCount = new int[mzSearchChunk.Count];
// Pointer into .SurveyScans
var fullSICScanIndices = new int[mzSearchChunk.Count, scanList.SurveyScans.Count];
var fullSICIntensities = new double[mzSearchChunk.Count, scanList.SurveyScans.Count];
var fullSICMasses = new double[mzSearchChunk.Count, scanList.SurveyScans.Count];
// The following is a 1D array, containing the SIC intensities for a single m/z group
var fullSICIntensities1D = new double[scanList.SurveyScans.Count];
// Initialize .MaximumIntensity and .ScanIndexMax
// Additionally, reset fullSICDataCount() and, for safety, set fullSICScanIndices() to -1
for (var mzIndexWork = 0; mzIndexWork < mzSearchChunk.Count; mzIndexWork++)
{
mzSearchChunk[mzIndexWork].ResetMaxIntensity();
fullSICDataCount[mzIndexWork] = 0;
for (var surveyScanIndex = 0; surveyScanIndex < scanList.SurveyScans.Count; surveyScanIndex++)
{
fullSICScanIndices[mzIndexWork, surveyScanIndex] = -1;
}
}
// ---------------------------------------------------------
// Step through scanList to obtain the scan numbers and intensity data for each .SearchMZ in udtMZSearchChunk
// We're stepping scan by scan since the process of loading a scan from disk is slower than the process of searching for each m/z in the scan
// ---------------------------------------------------------
for (var surveyScanIndex = 0; surveyScanIndex < scanList.SurveyScans.Count; surveyScanIndex++)
{
bool useScan;
if (processSIMScans)
{
useScan = scanList.SurveyScans[surveyScanIndex].SIMScan &&
scanList.SurveyScans[surveyScanIndex].SIMIndex == simIndex;
}
else
{
useScan = !scanList.SurveyScans[surveyScanIndex].SIMScan;
if (scanList.SurveyScans[surveyScanIndex].ZoomScan)
{
useScan = false;
}
}
if (!useScan)
{
continue;
}
if (!spectraCache.GetSpectrum(scanList.SurveyScans[surveyScanIndex].ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.MasicErrorCodes.ErrorUncachingSpectrum);
return false;
}
for (var mzIndexWork = 0; mzIndexWork < mzSearchChunk.Count; mzIndexWork++)
{
var current = mzSearchChunk[mzIndexWork];
double mzToleranceDa;
if (current.MZToleranceIsPPM)
{
mzToleranceDa = Utilities.PPMToMass(current.MZTolerance, current.SearchMZ);
}
else
{
mzToleranceDa = current.MZTolerance;
}
var ionSum = dataAggregation.AggregateIonsInRange(
spectrum,
current.SearchMZ, mzToleranceDa,
out _, out var closestMZ, false);
var dataIndex = fullSICDataCount[mzIndexWork];
fullSICScanIndices[mzIndexWork, dataIndex] = surveyScanIndex;
fullSICIntensities[mzIndexWork, dataIndex] = ionSum;
if (ionSum < float.Epsilon && masicOptions.SICOptions.ReplaceSICZeroesWithMinimumPositiveValueFromMSData)
{
fullSICIntensities[mzIndexWork, dataIndex] = scanList.SurveyScans[surveyScanIndex].MinimumPositiveIntensity;
}
fullSICMasses[mzIndexWork, dataIndex] = closestMZ;
if (ionSum > current.MaximumIntensity)
{
current.MaximumIntensity = ionSum;
current.ScanIndexMax = dataIndex;
}
fullSICDataCount[mzIndexWork]++;
}
if (surveyScanIndex % 100 == 0)
{
var subtaskPercentComplete = ComputeMzSearchChunkProgress(
parentIonsProcessed, scanList.ParentIons.Count,
surveyScanIndex, scanList.SurveyScans.Count, mzSearchChunkProgressFraction);
var progressMessage = "Loading raw SIC data: " + surveyScanIndex + " / " + scanList.SurveyScans.Count;
UpdateProgress(subtaskPercentComplete, progressMessage);
if (masicOptions.AbortProcessing)
{
scanList.ProcessingIncomplete = true;
return false;
}
}
}
UpdateProgress(CREATING_SICS);
if (masicOptions.AbortProcessing)
{
scanList.ProcessingIncomplete = true;
return false;
}
const int debugParentIonIndexToFind = 3139;
const float DebugMZToFind = 488.47F;
// ---------------------------------------------------------
// Compute the noise level in fullSICIntensities() for each m/z in udtMZSearchChunk
// Also, find the peaks for each m/z in udtMZSearchChunk and retain the largest peak found
// ---------------------------------------------------------
for (var mzIndexWork = 0; mzIndexWork < mzSearchChunk.Count; mzIndexWork++)
{
// Use this for debugging
if (Math.Abs(mzSearchChunk[mzIndexWork].SearchMZ - DebugMZToFind) < 0.1)
{
// ReSharper disable once UnusedVariable
var parentIonIndexPointer = mzSearchChunk[mzIndexWork].MZIndexStart;
}
// Copy the data for this m/z into fullSICIntensities1D()
for (var dataIndex = 0; dataIndex < fullSICDataCount[mzIndexWork]; dataIndex++)
{
fullSICIntensities1D[dataIndex] = fullSICIntensities[mzIndexWork, dataIndex];
}
// Compute the noise level; the noise level may change with increasing index number if the background is increasing for a given m/z
var success = mMASICPeakFinder.ComputeDualTrimmedNoiseLevelTTest(
fullSICIntensities1D, 0, fullSICDataCount[mzIndexWork] - 1,
masicOptions.SICOptions.SICPeakFinderOptions.SICBaselineNoiseOptions,
out var noiseStatSegments);
if (!success)
{
SetLocalErrorCode(clsMASIC.MasicErrorCodes.FindSICPeaksError, true);
return false;
}
mzSearchChunk[mzIndexWork].BaselineNoiseStatSegments = noiseStatSegments;
// Compute the minimum potential peak area in the entire SIC, populating udtSICPotentialAreaStatsInFullSIC
mMASICPeakFinder.FindPotentialPeakArea(
fullSICDataCount[mzIndexWork],
fullSICIntensities1D,
out var potentialAreaStatsInFullSIC,
masicOptions.SICOptions.SICPeakFinderOptions);
var scanIndexObservedInFullSIC = mzSearchChunk[mzIndexWork].ScanIndexMax;
// Initialize sicDetails
var sicDetails = new SICDetails
{
SICScanType = ScanList.ScanTypeConstants.SurveyScan
};
// Populate sicDetails using the data centered around the highest intensity in fullSICIntensities
// Note that this function will update sicPeak.IndexObserved
var sicPeak = ExtractSICDetailsFromFullSIC(
mzIndexWork, mzSearchChunk[mzIndexWork].BaselineNoiseStatSegments,
fullSICDataCount[mzIndexWork], fullSICScanIndices, fullSICIntensities, fullSICMasses,
scanList, scanIndexObservedInFullSIC,
sicDetails,
masicOptions, scanNumScanConverter, false, 0);
UpdateSICStatsUsingLargestPeak(
sicDetails,
sicPeak,
masicOptions,
potentialAreaStatsInFullSIC,
scanList,
mzSearchChunk,
mzIndexWork,
parentIonIndices,
debugParentIonIndexToFind,
dataOutputHandler,
xmlResultsWriter,
parentIonUpdated,
ref parentIonsProcessed);
// --------------------------------------------------------
// Now step through the parent ions and process those that were not updated using sicPeak
// For each, search for the closest peak in SICIntensity
// --------------------------------------------------------
for (var parentIonIndexPointer = mzSearchChunk[mzIndexWork].MZIndexStart; parentIonIndexPointer <= mzSearchChunk[mzIndexWork].MZIndexEnd; parentIonIndexPointer++)
{
if (parentIonUpdated[parentIonIndexPointer])
continue;
if (parentIonIndices[parentIonIndexPointer] == debugParentIonIndexToFind)
{
// ReSharper disable once RedundantAssignment
scanIndexObservedInFullSIC = -1;
}
var currentParentIon = scanList.ParentIons[parentIonIndices[parentIonIndexPointer]];