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clsScanTracking.cs
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clsScanTracking.cs
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using System;
using System.Collections.Generic;
using MASIC.DatasetStats;
using MASIC.Options;
using MASICPeakFinder;
namespace MASIC
{
/// <summary>
/// Class for tracking scan metadata
/// </summary>
public class clsScanTracking : clsMasicEventNotifier
{
/// <summary>
/// Absolute maximum number of ions that will be tracked for a mass spectrum
/// </summary>
private const int MAX_ALLOWABLE_ION_COUNT = 50000;
/// <summary>
/// Scan Stats list
/// </summary>
public List<ScanStatsEntry> ScanStats { get; }
private readonly clsReporterIons mReporterIons;
private readonly clsMASICPeakFinder mPeakFinder;
private int mSpectraFoundExceedingMaxIonCount;
private int mMaxIonCountReported;
/// <summary>
/// Constructor
/// </summary>
/// <param name="reporterIons"></param>
/// <param name="peakFinder"></param>
public clsScanTracking(clsReporterIons reporterIons, clsMASICPeakFinder peakFinder)
{
mReporterIons = reporterIons;
mPeakFinder = peakFinder;
ScanStats = new List<ScanStatsEntry>();
}
/// <summary>
/// Check whether the scan number is within the range specified by sicOptions
/// </summary>
/// <param name="scanNumber"></param>
/// <param name="sicOptions"></param>
/// <returns>True if filtering is disabled, or if scanNumber is within the limits</returns>
public bool CheckScanInRange(
int scanNumber,
SICOptions sicOptions)
{
if (sicOptions.ScanRangeStart >= 0 && sicOptions.ScanRangeEnd > sicOptions.ScanRangeStart)
{
if (scanNumber < sicOptions.ScanRangeStart || scanNumber > sicOptions.ScanRangeEnd)
{
return false;
}
}
return true;
}
/// <summary>
/// Check whether the scan number and elution time are within the ranges specified by sicOptions
/// </summary>
/// <param name="scanNumber"></param>
/// <param name="elutionTime"></param>
/// <param name="sicOptions"></param>
/// <returns>True if filtering is disabled, or if scanNumber and elutionTime are within the limits</returns>
public bool CheckScanInRange(
int scanNumber,
double elutionTime,
SICOptions sicOptions)
{
if (!CheckScanInRange(scanNumber, sicOptions))
{
return false;
}
if (sicOptions.RTRangeStart >= 0 && sicOptions.RTRangeEnd > sicOptions.RTRangeStart)
{
if (elutionTime < sicOptions.RTRangeStart || elutionTime > sicOptions.RTRangeEnd)
{
return false;
}
}
return true;
}
/// <summary>
/// Resizes the lists to a set capacity (unless there are existing contents larger than <paramref name="scanCount"/>)
/// </summary>
/// <param name="scanCount"></param>
public void ReserveListCapacity(int scanCount)
{
ScanStats.Capacity = Math.Max(ScanStats.Count, scanCount);
}
/// <summary>
/// Reduces memory usage by resizing the list to the contents
/// </summary>
public void SetListCapacityToCount()
{
ScanStats.Capacity = ScanStats.Count;
}
private void CompressSpectraData(
clsMSSpectrum msSpectrum,
double msDataResolution,
double mzIgnoreRangeStart,
double mzIgnoreRangeEnd)
{
// First, look for blocks of data points that consecutively have an intensity value of 0
// For each block of data found, reduce the data to only retain the first data point and last data point in the block
//
// Next, look for data points in msSpectrum that are within msDataResolution units of one another (m/z units)
// If found, combine into just one data point, keeping the largest intensity and the m/z value corresponding to the largest intensity
if (msSpectrum.IonCount <= 1)
{
return;
}
// Look for blocks of data points that all have an intensity value of 0
var targetIndex = 0;
var index = 0;
while (index < msSpectrum.IonCount)
{
if (msSpectrum.IonsIntensity[index] < float.Epsilon)
{
var countCombined = 0;
for (var comparisonIndex = index + 1; comparisonIndex < msSpectrum.IonCount; comparisonIndex++)
{
if (msSpectrum.IonsIntensity[comparisonIndex] < float.Epsilon)
{
countCombined++;
}
else
{
break;
}
}
if (countCombined > 1)
{
// Only keep the first and last data point in the block
msSpectrum.IonsMZ[targetIndex] = msSpectrum.IonsMZ[index];
msSpectrum.IonsIntensity[targetIndex] = msSpectrum.IonsIntensity[index];
targetIndex++;
msSpectrum.IonsMZ[targetIndex] = msSpectrum.IonsMZ[index + countCombined];
msSpectrum.IonsIntensity[targetIndex] = msSpectrum.IonsIntensity[index + countCombined];
index += countCombined;
}
// Keep this data point since a single zero
else if (targetIndex != index)
{
msSpectrum.IonsMZ[targetIndex] = msSpectrum.IonsMZ[index];
msSpectrum.IonsIntensity[targetIndex] = msSpectrum.IonsIntensity[index];
}
}
// Note: targetIndex will be the same as index until the first time that data is combined (countCombined > 0)
// After that, targetIndex will always be less than index and we will thus always need to copy data
else if (targetIndex != index)
{
msSpectrum.IonsMZ[targetIndex] = msSpectrum.IonsMZ[index];
msSpectrum.IonsIntensity[targetIndex] = msSpectrum.IonsIntensity[index];
}
index++;
targetIndex++;
}
// Update .IonCount with the new data count
msSpectrum.ShrinkArrays(targetIndex);
// Step through the data, consolidating data within msDataResolution
// Note that we're copying in place rather than making a new, duplicate array
// If the m/z value is between mzIgnoreRangeStart and mzIgnoreRangeEnd, we will not compress the data
targetIndex = 0;
index = 0;
while (index < msSpectrum.IonCount)
{
var countCombined = 0;
var bestMz = msSpectrum.IonsMZ[index];
// Only combine data if the first data point has a positive intensity value
if (msSpectrum.IonsIntensity[index] > 0)
{
var pointInIgnoreRange = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[index], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointInIgnoreRange)
{
for (var comparisonIndex = index + 1; comparisonIndex < msSpectrum.IonCount; comparisonIndex++)
{
if (clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[comparisonIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd))
{
// Reached the ignore range; do not allow to be combined with the current data point
break;
}
if (msSpectrum.IonsMZ[comparisonIndex] - msSpectrum.IonsMZ[index] < msDataResolution)
{
if (msSpectrum.IonsIntensity[comparisonIndex] > msSpectrum.IonsIntensity[index])
{
msSpectrum.IonsIntensity[index] = msSpectrum.IonsIntensity[comparisonIndex];
bestMz = msSpectrum.IonsMZ[comparisonIndex];
}
countCombined++;
}
else
{
break;
}
}
}
}
// Note: targetIndex will be the same as index until the first time that data is combined (countCombined > 0)
// After that, targetIndex will always be less than index and we will thus always need to copy data
if (targetIndex != index || countCombined > 0)
{
msSpectrum.IonsMZ[targetIndex] = bestMz;
msSpectrum.IonsIntensity[targetIndex] = msSpectrum.IonsIntensity[index];
index += countCombined;
}
index++;
targetIndex++;
}
// Update .IonCount with the new data count
msSpectrum.ShrinkArrays(targetIndex);
}
private void ComputeNoiseLevelForMassSpectrum(
clsScanInfo scanInfo,
clsMSSpectrum msSpectrum,
clsBaselineNoiseOptions noiseThresholdOptions)
{
const bool IGNORE_NON_POSITIVE_DATA = true;
scanInfo.BaselineNoiseStats = clsMASICPeakFinder.InitializeBaselineNoiseStats(0, noiseThresholdOptions.BaselineNoiseMode);
if (noiseThresholdOptions.BaselineNoiseMode == clsMASICPeakFinder.NoiseThresholdModes.AbsoluteThreshold)
{
scanInfo.BaselineNoiseStats.NoiseLevel = noiseThresholdOptions.BaselineNoiseLevelAbsolute;
scanInfo.BaselineNoiseStats.PointsUsed = 1;
}
else if (msSpectrum.IonCount > 0)
{
mPeakFinder.ComputeTrimmedNoiseLevel(
msSpectrum.IonsIntensity, 0, msSpectrum.IonCount - 1,
noiseThresholdOptions, IGNORE_NON_POSITIVE_DATA,
out var newBaselineNoiseStats);
scanInfo.BaselineNoiseStats = newBaselineNoiseStats;
}
}
/// <summary>
/// Process and store a spectrum
/// </summary>
/// <param name="scanInfo"></param>
/// <param name="dataImportUtilities"></param>
/// <param name="spectraCache"></param>
/// <param name="msSpectrum"></param>
/// <param name="noiseThresholdOptions"></param>
/// <param name="discardLowIntensityData"></param>
/// <param name="compressData"></param>
/// <param name="msDataResolution"></param>
/// <param name="keepRawSpectrum"></param>
/// <returns>True if success false if an error</returns>
public bool ProcessAndStoreSpectrum(
clsScanInfo scanInfo,
DataInput.clsDataImport dataImportUtilities,
clsSpectraCache spectraCache,
clsMSSpectrum msSpectrum,
clsBaselineNoiseOptions noiseThresholdOptions,
bool discardLowIntensityData,
bool compressData,
double msDataResolution,
bool keepRawSpectrum)
{
var lastKnownLocation = "Start";
try
{
// Determine the noise threshold intensity for this spectrum
// Stored in scanInfo.BaselineNoiseStats
lastKnownLocation = "Call ComputeNoiseLevelForMassSpectrum";
ComputeNoiseLevelForMassSpectrum(scanInfo, msSpectrum, noiseThresholdOptions);
if (!keepRawSpectrum)
{
return true;
}
// Discard low intensity data, but not for MRM scans
if (discardLowIntensityData && scanInfo.MRMScanType == ThermoRawFileReader.MRMScanTypeConstants.NotMRM)
{
// Discard data below the noise level or below the minimum S/N level
// If we are searching for Reporter ions, it is important to not discard any of the ions in the region of the reporter ion m/z values
lastKnownLocation = "Call DiscardDataBelowNoiseThreshold";
dataImportUtilities.DiscardDataBelowNoiseThreshold(msSpectrum,
scanInfo.BaselineNoiseStats.NoiseLevel,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd,
noiseThresholdOptions);
scanInfo.IonCount = msSpectrum.IonCount;
}
if (compressData)
{
lastKnownLocation = "Call CompressSpectraData";
// Again, if we are searching for Reporter ions, it is important to not discard any of the ions in the region of the reporter ion m/z values
CompressSpectraData(msSpectrum, msDataResolution,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd);
}
if (msSpectrum.IonCount > MAX_ALLOWABLE_ION_COUNT)
{
// Do not keep more than 50,000 ions
lastKnownLocation = "Call DiscardDataToLimitIonCount";
mSpectraFoundExceedingMaxIonCount++;
// Display a message at the console the first 10 times we encounter spectra with over MAX_ALLOWABLE_ION_COUNT ions
// In addition, display a new message every time a new max value is encountered
if (mSpectraFoundExceedingMaxIonCount <= 10 || msSpectrum.IonCount > mMaxIonCountReported)
{
Console.WriteLine();
Console.WriteLine(
"Note: Scan " + scanInfo.ScanNumber + " has " + msSpectrum.IonCount + " ions; " +
"will only retain " + MAX_ALLOWABLE_ION_COUNT + " (trimmed " +
mSpectraFoundExceedingMaxIonCount + " spectra)");
mMaxIonCountReported = msSpectrum.IonCount;
}
dataImportUtilities.DiscardDataToLimitIonCount(msSpectrum,
mReporterIons.MZIntensityFilterIgnoreRangeStart,
mReporterIons.MZIntensityFilterIgnoreRangeEnd,
MAX_ALLOWABLE_ION_COUNT);
scanInfo.IonCount = msSpectrum.IonCount;
}
lastKnownLocation = "Call AddSpectrumToPool";
return spectraCache.AddSpectrumToPool(msSpectrum, scanInfo.ScanNumber);
}
catch (Exception ex)
{
ReportError("Error in ProcessAndStoreSpectrum (LastKnownLocation: " + lastKnownLocation + ")", ex, clsMASIC.MasicErrorCodes.InputFileDataReadError);
return false;
}
}
}
}