/// <summary>
/// Reads the base peak chromatogram for the RAW file
/// </summary>
/// <param name="rawFile">
/// The RAW file being read
/// </param>
/// <param name="startScan">
/// Start scan for the chromatogram
/// </param>
/// <param name="endScan">
/// End scan for the chromatogram
/// </param>
/// <param name="outputData">
/// The output data flag.
/// </param>
/// <param name="filter">
/// The chromatic filter flag.
/// </param>
private static void GetChromatogram(IRawDataPlus rawFile, int startScan, int endScan, string filename, string filter = "ms")
{
if (IsValidFilter(rawFile, filter) == false)
{
Console.WriteLine("# '{0}' is not a valid filter string.", filter);
return;
}
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
// TODO([email protected]): check mass interval for chromatograms and its dep for diff MS detector types
// TODO([email protected]): return mass intervals to the R enviroment
// Define the settings for getting the Base Peak chromatogram
ChromatogramTraceSettings settingsTIC = new ChromatogramTraceSettings(TraceType.TIC)
{
Filter = filter
};
ChromatogramTraceSettings settingsBasePeak = new ChromatogramTraceSettings(TraceType.BasePeak)
{
Filter = filter,
MassRanges = new[] { ThermoFisher.CommonCore.Data.Business.Range.Create(100, 1805) }
};
ChromatogramTraceSettings settingsMassRange = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = filter,
MassRanges = new[] { ThermoFisher.CommonCore.Data.Business.Range.Create(50, 2000000) }
};
// Get the chromatogram from the RAW file.
var dataTIC = rawFile.GetChromatogramData(new IChromatogramSettings[] { settingsTIC }, startScan, endScan);
var dataMassRange = rawFile.GetChromatogramData(new IChromatogramSettings[] { settingsMassRange }, startScan, endScan);
var dataBasePeak = rawFile.GetChromatogramData(new IChromatogramSettings[] { settingsBasePeak }, startScan, endScan);
// Split the data into the chromatograms
var traceTIC = ChromatogramSignal.FromChromatogramData(dataTIC);
var traceMassRange = ChromatogramSignal.FromChromatogramData(dataMassRange);
var traceBasePeak = ChromatogramSignal.FromChromatogramData(dataBasePeak);
if (traceBasePeak[0].Length > 0)
{
// Print the chromatogram data (time, intensity values)
file.WriteLine("# TIC chromatogram ({0} points)", traceTIC[0].Length);
file.WriteLine("# Base Peak chromatogram ({0} points)", traceBasePeak[0].Length);
file.WriteLine("# MassRange chromatogram ({0} points)", traceMassRange[0].Length);
file.WriteLine("rt;intensity.BasePeak;intensity.TIC;intensity.MassRange");
for (int i = 0; i < traceBasePeak[0].Length; i++)
{
file.WriteLine("{1:F3};{2:F0};{3:F0};{4:F0}", i, traceBasePeak[0].Times[i], traceBasePeak[0].Intensities[i], traceTIC[0].Intensities[i], traceMassRange[0].Intensities[i]);
}
}
file.WriteLine();
}
}
public double[][] Data()
{
double[][] data = new double[2][];
// next make a request for the filtered chromatogram.
// Define settings for XIC
ChromatogramTraceSettings traceSettings =
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = filterMS,
MassRanges = new[] { new Range(mass, mass) }
};
// create the array of chromatogram settings
IChromatogramSettings[] allSettings = { traceSettings };
// set tolerance of +/- whatever ppm
MassOptions tolerance = new MassOptions()
{
Tolerance = ppm, ToleranceUnits = ToleranceUnits.ppm
};
// read the chromatogram
var chroData = rawFile.GetChromatogramData(allSettings, -1, -1, tolerance);
data[0] = chroData.PositionsArray.ToArray()[0];
data[1] = chroData.IntensitiesArray.ToArray()[0];
return(data);
}
public double[] GetXIC(double[] massList, double ppmError, string filter = "ms")
{
List <double> L = new List <double>();
List <ChromatogramTraceSettings> settingList = new List <ChromatogramTraceSettings>();
foreach (var mass in massList)
{
double massError = (0.5 * ppmError * mass) / 1000000;
ChromatogramTraceSettings settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = filter,
MassRanges = new[] { ThermoFisher.CommonCore.Data.Business.Range.Create(mass - massError, mass + massError) }
};
settingList.Add(settings);
}
IChromatogramSettings[] allSettings = settingList.ToArray();
var data = rawFile.GetChromatogramData(allSettings, this.GetFirstScanNumber(), this.GetLastScanNumber());
var traces = ChromatogramSignal.FromChromatogramData(data);
foreach (var t in traces)
{
foreach (int j in Enumerable.Range(0, t.Times.Count))
{
L.Add(t.Times[j]);
L.Add(t.Intensities[j]);
}
}
return(L.ToArray());
}
private static void GetXIC(IRawDataPlus rawFile, int startScan, int endScan, List <double> massList,
double ppmError, string filename)
{
List <ChromatogramTraceSettings> settingList = new List <ChromatogramTraceSettings>();
foreach (var mass in massList)
{
double massError = (0.5 * ppmError * mass) / 1000000;
ChromatogramTraceSettings settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = "ms",
MassRanges = new[] { Range.Create(mass - massError, mass + massError) }
};
settingList.Add(settings);
}
IChromatogramSettings[] allSettings = settingList.ToArray();
var data = rawFile.GetChromatogramData(allSettings, startScan, endScan);
/// compose JSON string
string json = "";
List <string> L = new List <string>();
// Split the data into the chromatograms
var trace = ChromatogramSignal.FromChromatogramData(data);
for (int i = 0; i < trace.Length; i++)
{
List <double> tTime = new List <double>();
List <double> tIntensities = new List <double>();
for (int j = 0; j < trace[i].Times.Count; j++)
{
if (trace[i].Intensities[j] > 0)
{
tTime.Add(trace[i].Times[j]);
tIntensities.Add(trace[i].Intensities[j]);
}
}
// file.WriteLine("\t{\n");
json = string.Format("\t\"mass\": {0},\n", massList[i]) +
string.Format("\t\"rt\": [\n\t\t\t" + string.Join(",\n\t\t\t", tTime) + "\n\t\t],") +
string.Format("\n\t\"intensities\": [\n\t\t\t" + string.Join(",\n\t\t\t", tIntensities) + "\n\t\t]");
L.Add("\t{\n" + json + "\n\t}");
}
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
file.WriteLine("[\n" + string.Join(",\n", L) + "\n]\n");
}
}
/// <summary>
/// Calculate the precursor peak intensity.
/// </summary>
/// <param name="rawFile">the RAW file object</param>
/// <param name="precursorScanNumber">the precursor scan number</param>
/// <param name="precursorMass">the precursor mass</param>
protected static double?CalculatePrecursorPeakIntensity(IRawDataPlus rawFile, int precursorScanNumber,
double precursorMass)
{
double?precursorIntensity = null;
// Get the scan from the RAW file
var scan = Scan.FromFile(rawFile, precursorScanNumber);
// Check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
var centroidStream = rawFile.GetCentroidStream(precursorScanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
if (Math.Abs(precursorMass - centroidStream.Masses[i]) < Tolerance)
{
//Console.WriteLine(Math.Abs(precursorMass - centroidStream.Masses[i]));
//Console.WriteLine(precursorMass + " - " + centroidStream.Masses[i] + " - " +
// centroidStream.Intensities[i]);
precursorIntensity = centroidStream.Intensities[i];
break;
}
}
}
}
else
{
rawFile.SelectInstrument(Device.MS, 1);
IChromatogramSettings[] allSettings =
{
new ChromatogramTraceSettings(TraceType.BasePeak)
{
Filter = MsFilter,
MassRanges = new[]
{
new Range(precursorMass, precursorMass)
}
}
};
var data = rawFile.GetChromatogramData(allSettings, precursorScanNumber,
precursorScanNumber);
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
if (!chromatogramTrace.IsNullOrEmpty())
{
precursorIntensity = chromatogramTrace[0].Intensities[0];
}
}
return(precursorIntensity);
}
/// <summary>
/// Get the spectrum intensity.
/// </summary>
/// <param name="rawFile">the RAW file object</param>
/// <param name="precursorScanNumber">the precursor scan number</param>
protected static double GetPrecursorIntensity(IRawDataPlus rawFile, int precursorScanNumber)
{
// Define the settings for getting the Base Peak chromatogram
var settings = new ChromatogramTraceSettings(TraceType.BasePeak);
// Get the chromatogram from the RAW file.
var data = rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, precursorScanNumber,
precursorScanNumber);
// Split the data into the chromatograms
var trace = ChromatogramSignal.FromChromatogramData(data);
return(trace[0].Intensities[0]);
}
private static IChromatogramData GetChromatogramData(IRawDataPlus rawFile, IChromatogramSettings settings,
int firstScanNumber, int lastScanNumber)
{
IChromatogramData data = null;
try
{
data = rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, firstScanNumber,
lastScanNumber);
}
catch (InvalidFilterFormatException ex)
{
Log.Warn($"Invalid filter string {settings.Filter}");
}
catch (InvalidFilterCriteriaException ex)
{
Log.Warn($"Invalid filter string {settings.Filter}");
}
return(data);
}
/// <summary>
/// Get and set chromatogram data from the raw file
/// </summary>
/// <param name="inputRawFile"></param>
private void GetChromatogramData(IRawDataPlus inputRawFile)
{
try
{
//Get mass resolution for the run from the header
MassResolution = inputRawFile.RunHeaderEx.MassResolution;
// Find startScan and endScan
int startScan = inputRawFile.RunHeader.FirstSpectrum;
int endScan = inputRawFile.RunHeader.LastSpectrum;
//Set up settings to extract the data
ChromatogramTraceSettings traceSettings =
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = FILTER_MS,
MassRanges = new[] { new Range(LowMass, HighMass) }
};
IChromatogramSettings[] allSettings = { traceSettings };
MassOptions massOptions = new MassOptions()
{
Tolerance = Tolerance, ToleranceUnits = ToleranceUnits
};
var chromatogramData = inputRawFile.GetChromatogramData(allSettings, startScan, endScan, massOptions); //get all chromatogram data
// Get data from the chromatogram
ScanNumList = chromatogramData.ScanNumbersArray[0];
ExactMassList = chromatogramData.PositionsArray[0]; //get positions of each scan
MassIntensityList = chromatogramData.IntensitiesArray[0]; //get list of intensities for scan numbers
}
catch (Exception ex)
{
Console.Write("Error in accessing chromatogram data: " + ex);
}
}
/// <summary>
/// Construct the chromatogram element(s)
/// </summary>
/// <param name="firstScanNumber">the first scan number</param>
/// <param name="lastScanNumber">the last scan number</param>
/// <returns>a list of chromatograms</returns>
private List <ChromatogramType> ConstructChromatograms(int firstScanNumber, int lastScanNumber)
{
var chromatograms = new List <ChromatogramType>();
// Define the settings for getting the Base Peak chromatogram
var settings = new ChromatogramTraceSettings(TraceType.BasePeak);
// Get the chromatogram from the RAW file.
var data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, firstScanNumber,
lastScanNumber);
// Split the data into the chromatograms
var trace = ChromatogramSignal.FromChromatogramData(data);
for (var i = 0; i < trace.Length; i++)
{
if (trace[i].Length > 0)
{
// Binary data array list
var binaryData = new List <BinaryDataArrayType>();
var chromatogram = new ChromatogramType
{
index = i.ToString(),
id = "base_peak_" + i,
defaultArrayLength = 0,
binaryDataArrayList = new BinaryDataArrayListType
{
count = "2",
binaryDataArray = new BinaryDataArrayType[2]
},
cvParam = new CVParamType[1]
};
chromatogram.cvParam[0] = new CVParamType
{
accession = "MS:1000235",
name = "total ion current chromatogram",
cvRef = "MS",
value = ""
};
// Chromatogram times
if (!trace[i].Times.IsNullOrEmpty())
{
// Set the chromatogram default array length
chromatogram.defaultArrayLength = trace[i].Times.Count;
var timesBinaryData =
new BinaryDataArrayType
{
binary = GetZLib64BitArray(trace[i].Times)
};
timesBinaryData.encodedLength =
(4 * Math.Ceiling((double)timesBinaryData
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
timesBinaryData.cvParam =
new CVParamType[3];
timesBinaryData.cvParam[0] =
new CVParamType
{
accession = "MS:1000595",
name = "time array",
cvRef = "MS",
unitName = "minute",
value = "",
unitCvRef = "UO",
unitAccession = "UO:0000031"
};
timesBinaryData.cvParam[1] =
new CVParamType
{
accession = "MS:1000523",
name = "64-bit float",
cvRef = "MS",
value = ""
};
timesBinaryData.cvParam[2] =
new CVParamType
{
accession = "MS:1000574",
name = "zlib compression",
cvRef = "MS",
value = ""
};
binaryData.Add(timesBinaryData);
}
// Chromatogram intensities
if (!trace[i].Times.IsNullOrEmpty())
{
// Set the spectrum default array length if necessary
if (chromatogram.defaultArrayLength == 0)
{
chromatogram.defaultArrayLength = trace[i].Intensities.Count;
}
var intensitiesBinaryData =
new BinaryDataArrayType
{
binary = GetZLib64BitArray(trace[i].Intensities)
};
intensitiesBinaryData.encodedLength =
(4 * Math.Ceiling((double)intensitiesBinaryData
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
intensitiesBinaryData.cvParam =
new CVParamType[3];
intensitiesBinaryData.cvParam[0] =
new CVParamType
{
accession = "MS:1000515",
name = "intensity array",
cvRef = "MS",
unitName = "number of counts",
value = "",
unitCvRef = "MS",
unitAccession = "MS:1000131"
};
intensitiesBinaryData.cvParam[1] =
new CVParamType
{
accession = "MS:1000523",
name = "64-bit float",
cvRef = "MS",
value = ""
};
intensitiesBinaryData.cvParam[2] =
new CVParamType
{
accession = "MS:1000574",
name = "zlib compression",
cvRef = "MS",
value = ""
};
binaryData.Add(intensitiesBinaryData);
}
if (!binaryData.IsNullOrEmpty())
{
chromatogram.binaryDataArrayList = new BinaryDataArrayListType
{
count = binaryData.Count.ToString(),
binaryDataArray = binaryData.ToArray()
};
}
chromatograms.Add(chromatogram);
}
}
return(chromatograms);
}
/// <summary>
/// Get the spectrum intensity.
/// </summary>
/// <param name="rawFile">the RAW file object</param>
/// <param name="precursorScanNumber">the precursor scan number</param>
/// <param name="precursorMass">the precursor mass</param>
/// <param name="retentionTime">the retention time</param>
/// <param name="isolationWidth">the isolation width</param>
protected static double? GetPrecursorIntensity(IRawDataPlus rawFile, int precursorScanNumber,
double precursorMass, double retentionTime, double? isolationWidth)
{
double? precursorIntensity = null;
// Get the scan from the RAW file
var scan = Scan.FromFile(rawFile, precursorScanNumber);
// Check if the scan has a centroid stream
if (scan.HasCentroidStream)
{
var centroidStream = rawFile.GetCentroidStream(precursorScanNumber, false);
if (scan.CentroidScan.Length > 0)
{
for (var i = 0; i < centroidStream.Length; i++)
{
if (Math.Abs(precursorMass - centroidStream.Masses[i]) < Tolerance)
{
//Console.WriteLine(Math.Abs(precursorMass - centroidStream.Masses[i]));
//Console.WriteLine(precursorMass + " - " + centroidStream.Masses[i] + " - " +
// centroidStream.Intensities[i]);
precursorIntensity = centroidStream.Intensities[i];
break;
}
}
}
}
else
{
rawFile.SelectInstrument(Device.MS, 1);
var component = new Component
{
MassRange = new Limit
{
Low = (double) (precursorMass - isolationWidth / 2),
High = (double) (precursorMass + isolationWidth / 2)
},
RtRange = new Limit
{
Low = rawFile.RetentionTimeFromScanNumber(precursorScanNumber),
High = rawFile.RetentionTimeFromScanNumber(precursorScanNumber)
}
};
;
IChromatogramSettings[] allSettings =
{
new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = Component.Filter,
MassRanges = new[]
{
new Range(component.MassRange.Low, component.MassRange.High)
}
}
};
var rtFilteredScans = rawFile.GetFilteredScansListByTimeRange("",
component.RtRange.Low,
component.RtRange.High);
var data = rawFile.GetChromatogramData(allSettings, rtFilteredScans[0],
rtFilteredScans[rtFilteredScans.Count - 1]);
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
}
return precursorIntensity;
}
private static void ExtractIonChromatogramAsRcode(IRawDataPlus rawFile, int startScan, int endScan, List <double> massList,
double ppmError, string filename, string filter = "ms")
{
if (IsValidFilter(rawFile, filter) == false)
{
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
file.WriteLine("e$error <- \"'{0}' is not a valid filter string.\";", filter);
}
return;
}
List <ChromatogramTraceSettings> settingList = new List <ChromatogramTraceSettings>();
foreach (var mass in massList)
{
double massError = (0.5 * ppmError * mass) / 1000000;
ChromatogramTraceSettings settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = filter,
MassRanges = new[] { ThermoFisher.CommonCore.Data.Business.Range.Create(mass - massError, mass + massError) }
};
settingList.Add(settings);
}
IChromatogramSettings[] allSettings = settingList.ToArray();
var data = rawFile.GetChromatogramData(allSettings, startScan, endScan);
// Split the data into the chromatograms
var trace = ChromatogramSignal.FromChromatogramData(data);
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
file.WriteLine("#R\n");
for (int i = 0; i < trace.Length; i++)
{
List <double> tTime = new List <double>();
List <double> tIntensities = new List <double>();
for (int j = 0; j < trace[i].Times.Count; j++)
{
// if (trace[i].Intensities[j] > 0)
{
tTime.Add(trace[i].Times[j]);
tIntensities.Add(trace[i].Intensities[j]);
}
}
file.WriteLine("e$chromatogram[[{0}]] <- list(", i + 1);
file.WriteLine("\tfilter = '{0}',", filter);
file.WriteLine("\tppm = {0},", ppmError);
file.WriteLine("\tmass = {0},", massList[i]);
file.WriteLine("\ttimes = c(" + string.Join(",", tTime) + "),");
file.WriteLine("\tintensities = c(" + string.Join(",", tIntensities) + ")");
file.WriteLine(");");
}
}
}
