public double[] GetTotalIonCurrent()
{
if (ChromatogramList == null)
{
return null;
}
using (var chromatogram = ChromatogramList.chromatogram(0, true))
{
if (chromatogram == null)
{
return null;
}
TimeIntensityPairList timeIntensityPairList = new TimeIntensityPairList();
chromatogram.getTimeIntensityPairs(ref timeIntensityPairList);
double[] intensities = new double[timeIntensityPairList.Count];
for (int i = 0; i < intensities.Length; i++)
{
intensities[i] = timeIntensityPairList[i].intensity;
}
return intensities;
}
}
private void TestPWiz(string strFilePath)
{
const bool RUN_BENCHMARKS = false;
try
{
var objPWiz2 = new MSDataFile(strFilePath);
Console.WriteLine("Spectrum count: " + objPWiz2.run.spectrumList.size());
Console.WriteLine();
if (objPWiz2.run.spectrumList.size() > 0)
{
var intSpectrumIndex = 0;
do
{
var oSpectrum = objPWiz2.run.spectrumList.spectrum(intSpectrumIndex, getBinaryData: true);
pwiz.CLI.data.CVParam param;
if (oSpectrum.scanList.scans.Count > 0)
{
if (clsProteowizardDataParser.TryGetCVParam(oSpectrum.scanList.scans[0].cvParams, pwiz.CLI.cv.CVID.MS_scan_start_time, out param))
{
var intScanNum = intSpectrumIndex + 1;
var dblStartTimeMinutes = param.timeInSeconds() / 60.0;
Console.WriteLine("ScanIndex " + intSpectrumIndex + ", Scan " + intScanNum + ", Elution Time " + dblStartTimeMinutes + " minutes");
}
}
// Use the following to determine info on this spectrum
if (clsProteowizardDataParser.TryGetCVParam(oSpectrum.cvParams, pwiz.CLI.cv.CVID.MS_ms_level, out param))
{
int.TryParse(param.value, out _);
}
// Use the following to get the MZs and Intensities
var oMZs = oSpectrum.getMZArray();
oSpectrum.getIntensityArray();
if (oMZs.data.Count > 0)
{
Console.WriteLine(" Data count: " + oMZs.data.Count);
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (RUN_BENCHMARKS)
{
double dblTIC1 = 0;
double dblTIC2 = 0;
var dtStartTime = default(DateTime);
var dtEndTime = default(DateTime);
double dtRunTimeSeconds1 = 0;
double dtRunTimeSeconds2 = 0;
const int LOOP_ITERATIONS = 2000;
// Note from Matt Chambers (matt.chambers42 at gmail)
// Repeatedly accessing items directly via oMZs.data() can be very slow
// With 700 points and 2000 iterations, it takes anywhere from 0.6 to 1.1 seconds to run from dtStartTime to dtEndTime
dtStartTime = DateTime.Now;
for (var j = 1; j <= LOOP_ITERATIONS; j++)
{
for (var intIndex = 0; intIndex <= oMZs.data.Count - 1; intIndex++)
{
dblTIC1 += oMZs.data[intIndex];
}
}
dtEndTime = DateTime.Now;
dtRunTimeSeconds1 = dtEndTime.Subtract(dtStartTime).TotalSeconds;
// The preferred method is to copy the data from .data to a locally-stored mzArray var
// With 700 points and 2000 iterations, it takes 0.016 seconds to run from dtStartTime to dtEndTime
dtStartTime = DateTime.Now;
for (var j = 1; j <= LOOP_ITERATIONS; j++)
{
var oMzArray = oMZs.data;
for (var intIndex = 0; intIndex <= oMzArray.Count - 1; intIndex++)
{
dblTIC2 += oMzArray[intIndex];
}
}
dtEndTime = DateTime.Now;
dtRunTimeSeconds2 = dtEndTime.Subtract(dtStartTime).TotalSeconds;
Console.WriteLine(" " + oMZs.data.Count + " points with " + LOOP_ITERATIONS + " iterations gives Runtime1=" + dtRunTimeSeconds1.ToString("0.0##") + " sec. vs. Runtime2=" + dtRunTimeSeconds2.ToString("0.0##") + " sec.");
if (Math.Abs(dblTIC1 - dblTIC2) > float.Epsilon)
{
Console.WriteLine(" TIC values don't agree; this is unexpected");
}
}
}
if (intSpectrumIndex < 25)
{
intSpectrumIndex += 1;
}
else
{
intSpectrumIndex += 50;
}
} while (intSpectrumIndex < objPWiz2.run.spectrumList.size());
}
if (objPWiz2.run.chromatogramList.size() > 0)
{
var intChromIndex = 0;
do
{
var oTimeIntensityPairList = new TimeIntensityPairList();
// Note that even for a small .Wiff file (1.5 MB), obtaining the Chromatogram list will take some time (20 to 60 seconds)
// The chromatogram at index 0 should be the TIC
// The chromatogram at index >=1 will be each SRM
var oChromatogram = objPWiz2.run.chromatogramList.chromatogram(intChromIndex, getBinaryData: true);
// Determine the chromatogram type
if (clsProteowizardDataParser.TryGetCVParam(oChromatogram.cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out var param))
{
// Obtain the data
oChromatogram.getTimeIntensityPairs(ref oTimeIntensityPairList);
}
if (clsProteowizardDataParser.TryGetCVParam(oChromatogram.cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out param))
{
// Obtain the SRM scan
oChromatogram.getTimeIntensityPairs(ref oTimeIntensityPairList);
}
intChromIndex += 1;
} while (intChromIndex < 50 && intChromIndex < objPWiz2.run.chromatogramList.size());
}
}
catch (Exception ex)
{
OnErrorEvent("Error using ProteoWizard reader: " + ex.Message, ex);
}
}
/// <summary>
/// Gets the retention times from the first chromatogram in the data file.
/// Returns null if there are no chromatograms in the file.
/// </summary>
public double[] GetScanTimes()
{
using (_perf.CreateTimer("GetScanTimes")) // Not L10N
{
if (ChromatogramList == null || ChromatogramList.empty())
{
return null;
}
using (var chromatogram = ChromatogramList.chromatogram(0, true))
{
if (chromatogram == null)
{
return null;
}
TimeIntensityPairList timeIntensityPairList = new TimeIntensityPairList();
chromatogram.getTimeIntensityPairs(ref timeIntensityPairList);
double[] times = new double[timeIntensityPairList.Count];
for (int i = 0; i < times.Length; i++)
{
times[i] = timeIntensityPairList[i].time;
}
return times;
}
}
}
