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());
}
/// <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();
}
}
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>
/// 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]);
}
/// <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);
}
private void UpdateChromatogramData()
{
ChromatogramTraceSettings traceSettings;
MassOptions tolerance = null;
string msFilter;
if (ChroMsLevelComboBox.Text == "MS1" | ChroMsLevelComboBox.SelectedIndex == -1)
{
msFilter = "ms";
}
else if (ChroMsLevelComboBox.Text == "MS2")
{
msFilter = "ms2";
}
else if (ChroMsLevelComboBox.Text == "MS3")
{
msFilter = "ms3";
}
else
{
msFilter = String.Empty;
}
if (ChroTICRadioButton.Checked)
{
traceSettings = new ChromatogramTraceSettings(TraceType.TIC);
}
else if (ChroBPRadioButton.Checked)
{
traceSettings = new ChromatogramTraceSettings(TraceType.BasePeak);
}
else
{
if (ChroXICmzTextBox.Text.IsNullOrEmpty() || ChroXICmzTextBox.BackColor == Color.Red || ChroXICmzTextBox.Text == "")
{
traceSettings = new ChromatogramTraceSettings(TraceType.TIC);
}
else
{
double da = Convert.ToDouble(ChroXICmzTextBox.Text);
traceSettings = new ChromatogramTraceSettings(TraceType.MassRange)
{
MassRanges = new[] { new Range(da, da) },
};
if (!chroXICToleranceTextBox.Text.IsNullOrEmpty() && !(chroXICToleranceTextBox.BackColor == Color.Red) && !(chroXICToleranceTextBox.Text == ""))
{
tolerance = new MassOptions()
{
Tolerance = Convert.ToDouble(chroXICToleranceTextBox.Text)
};
if (chroMassTolPPM.Checked)
{
tolerance.ToleranceUnits = ToleranceUnits.ppm;
}
else if (chroMassTolDa.Checked)
{
tolerance.ToleranceUnits = ToleranceUnits.amu;
}
else
{
tolerance.ToleranceUnits = ToleranceUnits.mmu;
}
}
}
}
traceSettings.Filter = msFilter;
IChromatogramSettingsEx[] allSettings = { traceSettings };
ChromatogramData = RawData.GetChromatogramDataEx(allSettings, -1, -1, tolerance);
}
public static void ReadXic(string rawFilePath, bool base64, XicData xicData)
{
IRawDataPlus rawFile;
using (rawFile = RawFileReaderFactory.ReadFile(rawFilePath))
{
if (!rawFile.IsOpen)
{
throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
throw new RawFileParserException(
$"Error opening ({rawFile.FileError}) - {rawFilePath}");
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
throw new RawFileParserException("RAW file still being acquired - " + rawFilePath);
}
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);
// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
// Get the mass range from the RAW file
var minMass = rawFile.RunHeaderEx.LowMass;
var maxMass = rawFile.RunHeaderEx.HighMass;
// Update global metadata
xicData.OutputMeta.base64 = base64;
xicData.OutputMeta.timeunit = "minutes";
foreach (var xicUnit in xicData.Content)
{
IChromatogramSettings settings = null;
if (!xicUnit.Meta.MzStart.HasValue && !xicUnit.Meta.MzEnd.HasValue)
{
settings = new ChromatogramTraceSettings()
{
Filter = xicUnit.Meta.Filter ?? "ms"
};
}
if (!xicUnit.Meta.MzStart.HasValue)
{
xicUnit.Meta.MzStart = minMass;
}
if (!xicUnit.Meta.MzEnd.HasValue)
{
xicUnit.Meta.MzEnd = maxMass;
}
if (settings == null)
{
settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = xicUnit.Meta.Filter ?? "ms",
MassRanges = new[]
{
new Range(xicUnit.Meta.MzStart.Value,
xicUnit.Meta.MzEnd.Value)
}
};
}
List <int> rtFilteredScans = null;
if (!xicUnit.Meta.RtStart.HasValue && !xicUnit.Meta.RtEnd.HasValue)
{
rtFilteredScans = new List <int>();
}
if (!xicUnit.Meta.RtStart.HasValue)
{
xicUnit.Meta.RtStart = startTime;
}
if (!xicUnit.Meta.RtEnd.HasValue)
{
xicUnit.Meta.RtEnd = endTime;
}
IChromatogramData data = null;
if (rtFilteredScans == null)
{
rtFilteredScans = rawFile.GetFilteredScansListByTimeRange(MsFilter,
xicUnit.Meta.RtStart.Value, xicUnit.Meta.RtEnd.Value);
if (rtFilteredScans.Count != 0)
{
data = GetChromatogramData(rawFile, settings, rtFilteredScans[0],
rtFilteredScans[rtFilteredScans.Count - 1]);
if (data != null && data.PositionsArray.Length == 1 && data.PositionsArray[0].Length == 1 &&
(Math.Abs(data.PositionsArray[0][0] - startTime) < 0.001 ||
Math.Abs(data.PositionsArray[0][0] - endTime) < 0.001))
{
Log.Warn(
$"Only the minimum or maximum retention time was returned. This is an indication that the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
Log.Warn(
$"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. This is an indication that the provided retention time window lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
data = GetChromatogramData(rawFile, settings, firstScanNumber, lastScanNumber);
}
if (data != null)
{
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
if (chromatogramTrace[0].Scans.Count != 0)
{
if (!base64)
{
xicUnit.RetentionTimes = chromatogramTrace[0].Times;
xicUnit.Intensities = chromatogramTrace[0].Intensities;
}
else
{
xicUnit.RetentionTimes = GetBase64String(chromatogramTrace[0].Times);
xicUnit.Intensities = GetBase64String(chromatogramTrace[0].Intensities);
}
}
}
}
}
}
private static void ExtractIonChromatogramAsRcode(IRawDataPlus rawFile, int startScan, int endScan, List <double> massList,
double ppmError, string filename, string filter = "ms")
{
if (IsValidFilter(rawFile, filter) == false)
{
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
file.WriteLine("e$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(");");
}
}
}
