/// <summary>
/// Illustrate how to use
/// GetSpectrum(double retentionTime, MSScanType scanType, IonPolarity ionPolarity, IonizationMode ionMode, IMsdrPeakFilter peakFilter, bool peakFilterOnCentroid);
/// Get a TIC, and then use the retention time array to access each scan.
/// </summary>
/// <param name="dataAccess"></param>
private void DoSpectrumExtractionTest(IMsdrDataReader dataAccess)
{
IMsdrPeakFilter filter1 = new MsdrPeakFilter();
filter1.AbsoluteThreshold = 10;
filter1.RelativeThreshold = 0.1;
filter1.MaxNumPeaks = 0;
IBDAChromFilter chromFilter = new BDAChromFilter();
chromFilter.ChromatogramType = ChromType.TotalIon;
chromFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;
IBDAChromData[] chroms = dataAccess.GetChromatogram(chromFilter);
IBDAChromData chrom = chroms[0];
double[] retTime = chrom.XArray;
for (int i = 0; i < retTime.Length; i++)
{
println("Extract spectrum at RT=" + retTime[i]);
//Get a spectrum without doing peak filtering if the spectrum is centroid
//The peak filter passed in will be applied to profile spectrum, but not
//centroid spectrum, because the flag peakFilterOnCentroid=false
IBDASpecData spec = dataAccess.GetSpectrum(retTime[i], MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, filter1, false);//peakFilterOnCentroid=false
/*//uncomment this section if you want to print out spectrum points
* double[] mzVals = spec.XArray;
* float[] aboundanceVals = spec.YArray;
* for (int j = 0; j < mzVals.Length; j++)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
*/
//Get a spectrum and apply peak filtering to it regardless profile or centroid
IBDASpecData spec2 = dataAccess.GetSpectrum(retTime[i], MSScanType.All, IonPolarity.Mixed, IonizationMode.Unspecified, filter1, true);//peakFilterOnCentroid=true
/*
* mzVals = spec.XArray;
* aboundanceVals = spec.YArray;
* for (int j = 0; j < mzVals.Length; j++)
* {
* if (aboundanceVals[j] > 5000)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
* }
*/
if (spec2.TotalDataPoints > spec.TotalDataPoints)
{//since spec2 is always thresholded, it must have less than or equal # of points as spec
println(" Error: filtered spectrum contains more points than unfiltered spectrum!");
}
}
}
public override int GetSpectrumNumber(double retentionTime)
{
IBDAChromData tic = _msdr.GetTIC();
int index = -1;
for (int i = 0; i < tic.TotalDataPoints; i++)
{
if (index < 0 || Math.Abs(tic.XArray[i] - retentionTime) < Math.Abs(tic.XArray[index] - retentionTime))
{
index = i;
}
}
return(index + 1);
}
// Extract non-MS data from the specified file path, with UV spectra limited to at
// most the specified number.
private void ExtractNonMSData(string dataFilePath, int maxSpectraToReport)
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(dataFilePath);
INonmsDataReader nonMsReader = dataReader as INonmsDataReader;
IDeviceInfo[] deviceInfo = nonMsReader.GetNonmsDevices();
if ((deviceInfo == null) || (deviceInfo.Length == 0))
{
println("No Non MS device found");
}
else
{
foreach (IDeviceInfo device in deviceInfo)
{
println("Device = " + device.DeviceName + " Ordinal number = " + device.OrdinalNumber.ToString() + " Device type = " + device.DeviceType.ToString());
#region DAD Signal & Spectrum
if (device.DeviceType == DeviceType.DiodeArrayDetector ||
device.DeviceType == DeviceType.HDR ||
device.DeviceType == DeviceType.CompactLC1220DAD)
{
//Extracting Signal Information
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.Chromatograms);
if (sigInfo.Length == 0)
{
println("No DAD signal found");
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendFormat("Found info on {0} signals: ", sigInfo.Length);
foreach (ISignalInfo info in sigInfo)
{
sb.AppendFormat("{0}, ", info.SignalName);
}
println(sb.ToString());
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No data found for first DAD signal");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// This information can be exported to a file on disk
FileStream file = new FileStream(@"C:\temp\reportNew.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
//Extracting TWC
IBDAChromData chromDataTWC = nonMsReader.GetTWC(device);
//compare this data with our own file
if ((chromDataTWC == null) || (chromDataTWC.TotalDataPoints == 0))
{
println("No TWC found");
}
else
{
int dataPoints = chromDataTWC.TotalDataPoints;
double[] xArrayTWC = chromDataTWC.XArray;
float[] yArrayTWC = chromDataTWC.YArray;
// Expoting this information to a file on disk
FileStream fileTWC = new FileStream(@"C:\temp\reportTWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swTWC = new StreamWriter(fileTWC);
swTWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayTWC.Length; i++)
{
swTWC.WriteLine(i.ToString() + "," + xArrayTWC[i].ToString() + "," + yArrayTWC[i].ToString());
}
swTWC.Close();
fileTWC.Close();
}
//Extracting EWC
IRange rangeSignal = new MinMaxRange(40, 250);
IRange rangeRef = new MinMaxRange(40, 250);
IBDAChromData chromDataEWC = nonMsReader.GetEWC(device, rangeSignal, rangeRef);
if ((chromDataEWC == null) || (chromDataEWC.TotalDataPoints == 0))
{
println("No EWC found");
}
else
{
double[] xArrayEWC = chromDataEWC.XArray;
float[] yArrayEWC = chromDataEWC.YArray;
// Expoting this information to a file on disk
FileStream fileEWC = new FileStream(@"C:\temp\reportEWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swEWC = new StreamWriter(fileEWC);
swEWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayEWC.Length; i++)
{
swEWC.WriteLine(i.ToString() + "," + xArrayEWC[i].ToString() + "," + yArrayEWC[i].ToString());
}
swEWC.Close();
fileEWC.Close();
}
//UV Spectrum: get each UV spectrum in the file
string uvSpectraFilePath = @"C:\temp\reportUV.csv";
if (File.Exists(uvSpectraFilePath))
{
File.Delete(uvSpectraFilePath);
}
for (int k = 0; k < chromDataTWC.XArray.Length && k < maxSpectraToReport; k++)
{
IRange range = new MinMaxRange(chromDataTWC.XArray[k], chromDataTWC.XArray[k]);
IBDASpecData[] uvSpecData = nonMsReader.GetUVSpectrum(device, range);
if (uvSpecData == null)
{
println("No UV spectrum found");
}
else
{
foreach (IBDASpecData uvSpec in uvSpecData)
{
if (uvSpec.TotalDataPoints != 0)
{
int dataPopints = uvSpec.TotalDataPoints;
double[] xArrayUV = uvSpec.XArray;
float[] yArrayUV = uvSpec.YArray;
// Expoting this information to a file on disk
FileStream fileUV = new FileStream(uvSpectraFilePath, FileMode.Append,
FileAccess.Write);
TextWriter swUV = new StreamWriter(fileUV);
swUV.WriteLine("#Point,X(Nanometers),Y(mAU)");
for (int i = 0; i < xArrayUV.Length; i++)
{
swUV.WriteLine(i.ToString() + "," + xArrayUV[i].ToString() + "," +
yArrayUV[i].ToString());
}
swUV.Close();
fileUV.Close();
}
else
{
println("No UV spectrum found");
}
}
}
}
}
#endregion
#region InstrumentCurves - TCC
if (device.DeviceType == DeviceType.ThermostattedColumnCompartment)
{
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.InstrumentCurves);
if (sigInfo.Length == 0)
{
println("No TCC Curves found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No TCC Curves found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// Expoting this information to a file on disk
FileStream file = new FileStream(@"C:\temp\reportInstrumentCurve.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
}
#endregion
}
}
}
/// <summary>
/// Get all Product Ion MS/MS scans and print out the precursor and collision energy.
/// </summary>
private void GetPrecursorInfo(IMsdrDataReader dataAccess)
{
//Create a chromatogram filter to let the scans that match
//the filter criteria to pass through
IBDAChromFilter chromFilter = new BDAChromFilter();
chromFilter.ChromatogramType = ChromType.TotalIon;
chromFilter.DesiredMSStorageType = DesiredMSStorageType.PeakElseProfile;//This means to use peak scans if available, otherwise use profile scans
chromFilter.MSLevelFilter = MSLevel.MSMS;
chromFilter.MSScanTypeFilter = MSScanType.ProductIon;
IBDAChromData[] chroms = dataAccess.GetChromatogram(chromFilter);//expect 1 chromatogram because we're not asking it to separate by scan segments, etc.
IBDAChromData chrom = chroms[0];
double[] retTime = chrom.XArray;
println("Get MS/MS spectra using retention time");
for (int i = 0; i < retTime.Length; i++)
{
//for each retention time, get the corresponding scan
//passing in null for peak filter means no peak threshold applied
IBDASpecData spec = dataAccess.GetSpectrum(retTime[i], MSScanType.ProductIon, IonPolarity.Mixed, IonizationMode.Unspecified, null);
print("RT=" + retTime[i] + ", ");
int precursorCount = 0;
double[] precursorIons = spec.GetPrecursorIon(out precursorCount);
if (precursorCount == 1)
{
print("Precursor Ions:");
for (int j = 0; j < precursorIons.Length; j++)
{
print(precursorIons[j] + " ");
}
println("");
int charge;
double intensity;
if (spec.GetPrecursorCharge(out charge))
{
println(" charge: " + charge);
}
else
{
println(" no charge avaialble");
}
if (spec.GetPrecursorIntensity(out intensity))
{
println(" intensity: " + intensity);
}
else
{
println(" no intensity available");
}
}
else
{
println("No precursor ions");
}
/*
* //Uncomment this if you want to print out x and y values of the spectrum.
* double[] mzVals = spec.XArray;
* float[] aboundanceVals = spec.YArray;
* println("RT=" + retTime[i]);
* for (int j = 0; j < mzVals.Length; j++)
* {
* println(mzVals[j] + ", " + aboundanceVals[j]);
* }
*/
}
}
/// <summary>
/// To extract non MS data
/// </summary>
private void ExtractNonMSData()
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(_NonMSdataFilename);
INonmsDataReader nonMsReader = dataReader as INonmsDataReader;
IDeviceInfo[] deviceInfo = nonMsReader.GetNonmsDevices();
if ((deviceInfo == null) || (deviceInfo.Length == 0))
{
println("No Non MS device found");
}
else
{
foreach (IDeviceInfo device in deviceInfo)
{
println("Device = " + device.DeviceName + " Ordinal number = " + device.OrdinalNumber.ToString() + " Device type = " + device.DeviceType.ToString());
#region DAD Signal & Spectrum
if (device.DeviceType == DeviceType.DiodeArrayDetector)
{
//Extracting Signal Information
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.Chromatograms);
if (sigInfo.Length == 0)
{
println("No DAD signal found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No DAD signal found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// This information can be exported to a file on disk
FileStream file = new FileStream(@"C:\temp\reportNew.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
//Extracting TWC
IBDAChromData chromDataTWC = nonMsReader.GetTWC(device);
//compare this data with our own file
if ((chromDataTWC == null) || (chromDataTWC.TotalDataPoints == 0))
{
println("No TWC found");
}
else
{
int dataPoints = chromDataTWC.TotalDataPoints;
double[] xArrayTWC = chromDataTWC.XArray;
float[] yArrayTWC = chromDataTWC.YArray;
// Expoting this information to a file on disk
FileStream fileTWC = new FileStream(@"C:\temp\reportTWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swTWC = new StreamWriter(fileTWC);
swTWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayTWC.Length; i++)
{
swTWC.WriteLine(i.ToString() + "," + xArrayTWC[i].ToString() + "," + yArrayTWC[i].ToString());
}
swTWC.Close();
fileTWC.Close();
}
//Extracting EWC
IRange rangeSignal = new MinMaxRange(40, 250);
IRange rangeRef = new MinMaxRange(40, 250);
IBDAChromData chromDataEWC = nonMsReader.GetEWC(device, rangeSignal, rangeRef);
if ((chromDataEWC == null) || (chromDataEWC.TotalDataPoints == 0))
{
println("No EWC signal found");
}
else
{
int dataPointsEWC = chromDataEWC.TotalDataPoints;
double[] xArrayEWC = chromDataEWC.XArray;
float[] yArrayEWC = chromDataEWC.YArray;
// Expoting this information to a file on disk
FileStream fileEWC = new FileStream(@"C:\temp\reportEWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swEWC = new StreamWriter(fileEWC);
swEWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayEWC.Length; i++)
{
swEWC.WriteLine(i.ToString() + "," + xArrayEWC[i].ToString() + "," + yArrayEWC[i].ToString());
}
swEWC.Close();
fileEWC.Close();
}
//UV Spectrum
IRange range = new MinMaxRange(1.109, 1.409);
IMinMaxRange ran = new MinMaxRange(1, 2);
ran.Max = 1;
IBDASpecData[] uvSpecData = nonMsReader.GetUVSpectrum(device, range);
if (uvSpecData == null)
{
println("No UV signal found");
}
else
{
foreach (IBDASpecData uvSpec in uvSpecData)
{
if (uvSpec.TotalDataPoints != 0)
{
int dataPopints = uvSpec.TotalDataPoints;
double[] xArrayUV = uvSpec.XArray;
float[] yArrayUV = uvSpec.YArray;
// Expoting this information to a file on disk
FileStream fileUV = new FileStream(@"C:\temp\reportUV.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swUV = new StreamWriter(fileUV);
swUV.WriteLine("#Point,X(Nanometers),Y(mAU)");
for (int i = 0; i < xArrayUV.Length; i++)
{
swUV.WriteLine(i.ToString() + "," + xArrayUV[i].ToString() + "," + yArrayUV[i].ToString());
}
swUV.Close();
fileUV.Close();
}
else
{
println("No UV signal found");
}
}
}
}
#endregion
#region InstrumentCurves - TCC
if (device.DeviceType == DeviceType.ThermostattedColumnCompartment)
{
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.InstrumentCurves);
if (sigInfo.Length == 0)
{
println("No TCC Curves found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No TCC Curves found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// Expoting this information to a file on disk
FileStream file = new FileStream(@"C:\temp\reportInstrumentCurve.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
}
#endregion
}
}
}
public double GetTotalIntensity()
{
IBDAChromData data = GetTIC();
return((double)data.YArray.Sum());
}