public void DiscardDataToLimitIonCount(
clsMSSpectrum msSpectrum,
double mzIgnoreRangeStart,
double mzIgnoreRangeEnd,
int maxIonCountToRetain)
{
// When this is true, will write a text file of the mass spectrum before and after it is filtered
// Enable this for debugging
var writeDebugData = false;
StreamWriter writer = null;
try
{
int ionCountNew;
if (msSpectrum.IonCount > maxIonCountToRetain)
{
var filterDataArray = new clsFilterDataArrayMaxCount
{
MaximumDataCountToKeep = maxIonCountToRetain,
TotalIntensityPercentageFilterEnabled = false
};
writeDebugData = false;
if (writeDebugData)
{
writer = new StreamWriter(new FileStream(Path.Combine(mOptions.OutputDirectoryPath, "DataDump_" + msSpectrum.ScanNumber.ToString() + "_BeforeFilter.txt"), FileMode.Create, FileAccess.Write, FileShare.Read));
writer.WriteLine("m/z" + "\t" + "Intensity");
}
// Store the intensity values in filterDataArray
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
filterDataArray.AddDataPoint(msSpectrum.IonsIntensity[ionIndex], ionIndex);
if (writeDebugData)
{
writer.WriteLine(msSpectrum.IonsMZ[ionIndex].ToString() + "\t" + msSpectrum.IonsIntensity[ionIndex]);
}
}
if (writeDebugData)
{
writer.Close();
}
// Call .FilterData, which will determine which data points to keep
filterDataArray.FilterData();
ionCountNew = 0;
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
// Always keep points in the m/z ignore range
// If CheckPointInMZIgnoreRange returns true, set pointPassesFilter to true
var pointPassesFilter = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[ionIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointPassesFilter)
{
// See if the point's intensity is negative
if (filterDataArray.GetAbundanceByIndex(ionIndex) >= 0)
{
pointPassesFilter = true;
}
}
if (pointPassesFilter)
{
msSpectrum.IonsMZ[ionCountNew] = msSpectrum.IonsMZ[ionIndex];
msSpectrum.IonsIntensity[ionCountNew] = msSpectrum.IonsIntensity[ionIndex];
ionCountNew += 1;
}
}
}
else
{
ionCountNew = msSpectrum.IonCount;
}
if (ionCountNew < msSpectrum.IonCount)
{
msSpectrum.ShrinkArrays(ionCountNew);
}
if (writeDebugData)
{
using (var postFilterWriter = new StreamWriter(new FileStream(Path.Combine(mOptions.OutputDirectoryPath, "DataDump_" + msSpectrum.ScanNumber.ToString() + "_PostFilter.txt"), FileMode.Create, FileAccess.Write, FileShare.Read)))
{
postFilterWriter.WriteLine("m/z" + "\t" + "Intensity");
// Store the intensity values in filterDataArray
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
postFilterWriter.WriteLine(msSpectrum.IonsMZ[ionIndex].ToString() + "\t" +
msSpectrum.IonsIntensity[ionIndex]);
}
}
}
}
catch (Exception ex)
{
ReportError("Error limiting the number of data points to " + maxIonCountToRetain, ex, clsMASIC.eMasicErrorCodes.UnspecifiedError);
}
}
/// <summary>
/// Discard data below the noise threshold
/// </summary>
/// <param name="msSpectrum"></param>
/// <param name="noiseThresholdIntensity"></param>
/// <param name="mzIgnoreRangeStart"></param>
/// <param name="mzIgnoreRangeEnd"></param>
/// <param name="noiseThresholdOptions"></param>
public void DiscardDataBelowNoiseThreshold(
clsMSSpectrum msSpectrum,
double noiseThresholdIntensity,
double mzIgnoreRangeStart,
double mzIgnoreRangeEnd,
MASICPeakFinder.clsBaselineNoiseOptions noiseThresholdOptions)
{
var ionCountNew = 0;
try
{
switch (noiseThresholdOptions.BaselineNoiseMode)
{
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.AbsoluteThreshold:
if (noiseThresholdOptions.BaselineNoiseLevelAbsolute > 0)
{
ionCountNew = 0;
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
// Always keep points in the m/z ignore range
// If CheckPointInMZIgnoreRange returns true, set pointPassesFilter to true
var pointPassesFilter = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[ionIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointPassesFilter)
{
// Check the point's intensity against .BaselineNoiseLevelAbsolute
if (msSpectrum.IonsIntensity[ionIndex] >= noiseThresholdOptions.BaselineNoiseLevelAbsolute)
{
pointPassesFilter = true;
}
}
if (pointPassesFilter)
{
msSpectrum.IonsMZ[ionCountNew] = msSpectrum.IonsMZ[ionIndex];
msSpectrum.IonsIntensity[ionCountNew] = msSpectrum.IonsIntensity[ionIndex];
ionCountNew += 1;
}
}
}
else
{
ionCountNew = msSpectrum.IonCount;
}
break;
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMeanByAbundance:
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMeanByCount:
case MASICPeakFinder.clsMASICPeakFinder.eNoiseThresholdModes.TrimmedMedianByAbundance:
if (noiseThresholdOptions.MinimumSignalToNoiseRatio > 0)
{
ionCountNew = 0;
for (var ionIndex = 0; ionIndex < msSpectrum.IonCount; ionIndex++)
{
// Always keep points in the m/z ignore range
// If CheckPointInMZIgnoreRange returns true, set pointPassesFilter to true
var pointPassesFilter = clsUtilities.CheckPointInMZIgnoreRange(msSpectrum.IonsMZ[ionIndex], mzIgnoreRangeStart, mzIgnoreRangeEnd);
if (!pointPassesFilter)
{
// Check the point's intensity against .BaselineNoiseLevelAbsolute
if (MASICPeakFinder.clsMASICPeakFinder.ComputeSignalToNoise(msSpectrum.IonsIntensity[ionIndex], noiseThresholdIntensity) >= noiseThresholdOptions.MinimumSignalToNoiseRatio)
{
pointPassesFilter = true;
}
}
if (pointPassesFilter)
{
msSpectrum.IonsMZ[ionCountNew] = msSpectrum.IonsMZ[ionIndex];
msSpectrum.IonsIntensity[ionCountNew] = msSpectrum.IonsIntensity[ionIndex];
ionCountNew += 1;
}
}
}
else
{
ionCountNew = msSpectrum.IonCount;
}
break;
default:
ReportError("Unknown BaselineNoiseMode encountered in DiscardDataBelowNoiseThreshold: " +
noiseThresholdOptions.BaselineNoiseMode.ToString());
break;
}
if (ionCountNew < msSpectrum.IonCount)
{
msSpectrum.ShrinkArrays(ionCountNew);
}
}
catch (Exception ex)
{
ReportError("Error discarding data below the noise threshold", ex, clsMASIC.eMasicErrorCodes.UnspecifiedError);
}
}
