/// <summary>
/// Open the given file and import scans into the reader.
/// </summary>
/// <returns></returns>
public System.Collections.IEnumerator GetEnumerator()
{
rawFile.SelectInstrument(ThermoBiz.Device.MS, 1);
// Get the first and last scan from the RAW file
int FirstScan = rawFile.RunHeaderEx.FirstSpectrum;
int LastScan = rawFile.RunHeaderEx.LastSpectrum;
for (int iScanNumber = FirstScan; iScanNumber <= LastScan; iScanNumber++)
{
ThermoBiz.Scan thermoScan = ThermoBiz.Scan.FromFile(rawFile, iScanNumber);
IScanFilter scanFilter = rawFile.GetFilterForScanNumber(iScanNumber);
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(iScanNumber);
if ((int)scanFilter.MSOrder == 1)
{
LastMS1 = iScanNumber;
}
Data.Scan scan = new Data.Scan()
{
ScanNumber = iScanNumber,
ScanEvent = (iScanNumber - LastMS1) + 1,
BasePeakIntensity = thermoScan.ScanStatistics.BasePeakIntensity,
BasePeakMz = thermoScan.ScanStatistics.BasePeakMass,
TotalIonCurrent = thermoScan.ScanStatistics.TIC,
LowestMz = thermoScan.ScanStatistics.LowMass,
HighestMz = thermoScan.ScanStatistics.HighMass,
StartMz = scanFilter.GetMassRange(0).Low,
EndMz = scanFilter.GetMassRange(0).High,
ScanType = ReadScanType(scanFilter.ToString()),
MsOrder = (int)scanFilter.MSOrder,
Polarity = (scanFilter.Polarity == PolarityType.Positive) ? Data.Polarity.Positive : Data.Polarity.Negative,
FilterLine = scanFilter.ToString(),
DetectorType = readDetectorType(scanFilter.MassAnalyzer),
RetentionTime = rawFile.RetentionTimeFromScanNumber(iScanNumber)
};
if (scan.MsOrder > 1)
{
// Get the current scan's activation method while ignoring upstream activation
scan.PrecursorActivationMethod = ConvertActivationType(scanFilter.GetActivation(scan.MsOrder - 2));
// handle dependent scans and not SPS (processed below)
scan.Precursors.Clear();
for (int i = 0; i < scanEvent.MassCount; ++i)
{
var reaction = scanEvent.GetReaction(i);
scan.CollisionEnergy = reaction.CollisionEnergy;
var precursor = new Data.Precursor
{
IsolationWidth = reaction.IsolationWidth,
IsolationMz = reaction.PrecursorMass,
Mz = reaction.PrecursorMass,
OriginalMz = reaction.PrecursorMass
};
scan.Precursors.Add(precursor);
}
}
ThermoBiz.RunHeader runHeader = rawFile.RunHeader;
ThermoBiz.LogEntry trailer = rawFile.GetTrailerExtraInformation(iScanNumber);
for (int i = 0; i < trailer.Length; i++)
{
var value = trailer.Values[i];
if (value == null)
{
continue;
}
switch (trailer.Labels[i])
{
case "Access ID":
int access_id = Convert.ToInt32(value);
if (access_id > 0)
{
scan.PrecursorMasterScanNumber = access_id;
}
break;
case "Scan Description:":
scan.Description = value.Trim();
break;
case "Ion Injection Time (ms):":
scan.IonInjectionTime = double.Parse(value);
break;
case "Elapsed Scan Time (sec):":
scan.ElapsedScanTime = double.Parse(value);
break;
case "Charge State:":
int charge = int.Parse(value);
foreach (var precursor in scan.Precursors)
{
precursor.Charge = charge;
precursor.OriginalCharge = precursor.Charge;
}
break;
case "Master Scan Number:":
scan.PrecursorMasterScanNumber = int.Parse(value);
break;
case "Master Index:":
scan.MasterIndex = int.Parse(value);
break;
case "Monoisotopic M/Z:":
if (Options.RawMonoMz && scan.Precursors.Count > 0)
{
double mz = double.Parse(value);
if (mz > 0)
{
scan.Precursors[0].Mz = mz;
}
}
break;
case "FAIMS CV:":
scan.FaimsCV = (int)double.Parse(value);
break;
case "FAIMS Voltage On:":
scan.FaimsState = (value == "No") ? Data.TriState.Off : Data.TriState.On;
break;
case "SPS Masses:":
string[] spsIonStringArray = value.TrimEnd(',').Split(',');
if (!string.IsNullOrWhiteSpace(spsIonStringArray[0]) && spsIonStringArray.Length > 0)
{
scan.Precursors.Clear();
for (int spsIndex = 0; spsIndex < spsIonStringArray.Length; spsIndex++)
{
if (double.TryParse(spsIonStringArray[spsIndex], out double spsIon))
{
scan.Precursors.Add(new Data.Precursor(spsIon, 0, 1));
}
}
}
break;
}
}
if (scan.PrecursorMasterScanNumber <= 0 && scan.MsOrder > 1)
{
// Try again to set the precursor scan.
SetPrecursorScanNumber(scan);
}
if (scan.MsOrder > 1 && scan.PrecursorMasterScanNumber > rawFile.RunHeader.FirstSpectrum && scan.PrecursorMasterScanNumber < rawFile.RunHeader.LastSpectrum)
{
// Fill precursor information
var parentScan = ThermoBiz.Scan.FromFile(rawFile, scan.PrecursorMasterScanNumber);
if (parentScan != null)
{
foreach (var precursor in scan.Precursors)
{
precursor.Intensity = GetMaxIntensity(parentScan, precursor.IsolationMz, precursor.IsolationWidth);
}
}
}
if (thermoScan.HasCentroidStream)
{
// High res data
CentroidsFromArrays(scan, thermoScan.CentroidScan.Masses, thermoScan.CentroidScan.Intensities, thermoScan.CentroidScan.Baselines, thermoScan.CentroidScan.Noises);
}
else
{
// Low res data
CentroidsFromArrays(scan, thermoScan.PreferredMasses, thermoScan.PreferredIntensities);
}
if (scan.PeakCount > 0)
{
scan.LowestMz = scan.Centroids[0].Mz;
scan.HighestMz = scan.Centroids[scan.PeakCount - 1].Mz;
}
yield return(scan);
}
}
//const String rawFile = @"E:\Python_1\meta\meta\bin\x64\Debug\10_Ile.RAW";
String rawFile = "20190924_ISmix21_pos_1_0.RAW";
//string resFilePath = "123kl.csv";
//string paraIndex = "3,4";
//const String filename = "E:/wamp/www/tp5/application/index/controller/21_Val.RAW";
//string filename = args[0];
//showheaderInfo(filename);
//string resFilePath = args[0];
//string rawFile = args[1];
//string paraIndex = args[2];
//string headerInfo = Encoding.UTF8.GetString(Encoding.Default.GetBytes(""));
//for (int i = 3; i < args.Length; i++)
//{
// headerInfo += Encoding.UTF8.GetString(Encoding.Default.GetBytes(args[i]));
//}
//getentityData(resFilePath, rawFile, headerInfo, paraIndex);
//getTuneInfo(filename);
getMSdataFromScanNum(46, 48, rawFile, 50, 500);
Console.ReadKey();
}
public static void getentityData(string resFilePath, string rawFile, string headerInfo, string paraIndex)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(rawFile);
plus.SelectInstrument(Device.MS, 1);
ArrayList indexOfpara = new ArrayList();
string[] selectIndex = paraIndex.Split(',');
foreach (string ele in selectIndex)
{
int index = Int32.Parse(ele);
indexOfpara.Add(index);
}
//string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(resFilePath, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
headerInfo = "RT," + headerInfo;
headerInfo = "#," + headerInfo;
writer.WriteLine(headerInfo);
int offset = 0;
int maxoffset = plus.GetStatusLogEntriesCount();
while (offset < maxoffset)
{
string temp = "";
IStatusLogEntry statusLogEntry = plus.GetStatusLogEntry(offset);
temp += offset.ToString() + ",";
temp += statusLogEntry.Time.ToString() + ",";
foreach (int ele in indexOfpara)
{
temp += Convert.ToString(statusLogEntry.Values[ele]) + ",";
}
writer.WriteLine(temp.Substring(0, temp.Length - 1));
offset += 1;
}
writer.Close();
}
public static void showheaderInfo(string filePath)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
HeaderItem[] statuslogheaderinformation = plus.GetStatusLogHeaderInformation();
int index = 0;
Console.OutputEncoding = Encoding.UTF8;
while (index < statuslogheaderinformation.Length)
{
Console.WriteLine(statuslogheaderinformation[index].Label);
//headerInfo[index] = statuslogheaderinformation[index].Label;
//writer.WriteLine(statuslogheaderinformation[index].Label);
index += 1;
}
//writer.Close();
//while (true)
//{
//if (index >= statuslogheaderinformation.Length)
//{
// Console.WriteLine(plus.RunHeaderEx.FirstSpectrum.ToString());
// Console.WriteLine(plus.RunHeaderEx.LastSpectrum.ToString());
// Console.WriteLine(plus.RunHeaderEx.StartTime.ToString("F2"));
// Console.WriteLine(plus.RunHeaderEx.EndTime.ToString("F2"));
// Console.WriteLine(plus.RunHeaderEx.LowMass.ToString());
// Console.WriteLine(plus.RunHeaderEx.HighMass.ToString());
// break;
//}
// Console.WriteLine(statuslogheaderinformation[index].Label);
// writer.WriteLine(statuslogheaderinformation[index].Label);
// index++;
//}
//writer.Close();
}
public static void getTuneInfo(string filePath)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".txt";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("*********************InstrumentMethod(0)***************************");
writer.WriteLine(plus.GetInstrumentMethod(0));
writer.WriteLine("*********************InstrumentMethod(1)****************************");
writer.WriteLine(plus.GetInstrumentMethod(1));
HeaderItem[] tuneDataHeaderInfo = plus.GetTuneDataHeaderInformation();
writer.WriteLine("*********************Tune DATA ****************************");
int tuneCnt = plus.GetTuneDataCount();
for (int i = 0; i < tuneDataHeaderInfo.Length; ++i)
{
writer.WriteLine(tuneDataHeaderInfo[i].Label);
}
writer.Close();
}
public static void getMSdataFromScanNum(int startNum, int endNum, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
//////////////////////////////////
plus.SelectInstrument(Device.MS, 1);
/////////////////////////////////
const string FilterStringIsolationMzPattern = @"ms2 (.*?)@";
int precursorMs1ScanNumber = 0;
double precursorMS= 0.00;
IReaction reaction = null;
var value = "";
var firstScanNumber = plus.RunHeaderEx.FirstSpectrum;
var lastScanNumber = plus.RunHeaderEx.LastSpectrum;
startNum = firstScanNumber;
endNum = lastScanNumber;
//int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
LimitedSizeDictionary<string, int> precursorMs2ScanNumbers = new LimitedSizeDictionary<string, int>(40);
plus.SelectInstrument(Device.MS, 1);
if(highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
double maxMs = plus.RunHeaderEx.HighMass;
double minMs = plus.RunHeaderEx.LowMass;
lowMS = minMs;
highMS = maxMs;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter,MSLevel,collisionEnergy, precursorNum,precursorMS");
while (startNum <= endNum)
{
var levelInfo = "";
var spectrumRef = "";
Scan scan = Scan.FromFile(plus, startNum);
IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum);
IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum);
switch (scanFilter.MSOrder)
{
case MSOrderType.Ms:
// Keep track of scan number for precursor reference
precursorMs1ScanNumber = startNum;
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + "" + "," + "" + "," + "";
break;
case MSOrderType.Ms2:
// Keep track of scan number and isolation m/z for precursor reference
var result = Regex.Match(scanEvent.ToString(), FilterStringIsolationMzPattern);
if (result.Success)
{
if (precursorMs2ScanNumbers.ContainsKey(result.Groups[1].Value))
{
precursorMs2ScanNumbers.Remove(result.Groups[1].Value);
}
precursorMs2ScanNumbers.Add(result.Groups[1].Value, startNum);
}
spectrumRef = precursorMs1ScanNumber.ToString();
reaction = scanEvent.GetReaction(0);
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
precursorMS = reaction.PrecursorMass;
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString() ;
break;
case MSOrderType.Ms3:
var precursorMs2ScanNumber = precursorMs2ScanNumbers.Keys.FirstOrDefault(isolationMz => scanEvent.ToString().Contains(isolationMz));
spectrumRef = precursorMs2ScanNumbers[precursorMs2ScanNumber].ToString();
if (!precursorMs2ScanNumber.IsNullOrEmpty())
{
reaction = scanEvent.GetReaction(1);
}
else
{
throw new InvalidOperationException("Couldn't find a MS2 precursor scan for MS3 scan " + scanEvent);
}
precursorMS = reaction.PrecursorMass;
value = reaction.CollisionEnergy.ToString(CultureInfo.InvariantCulture).ToString();
levelInfo = scanFilter.MSOrder.ToString() + "," + value + "," + spectrumRef.ToString() + "," + precursorMS.ToString();
break;
default:
throw new ArgumentOutOfRangeException();
}
//var scanStatistics = plus.GetScanStatsForScanNumber(startNum);
//// Get the segmented (low res and profile) scan data
//var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics);
//var masses = segmentedScan.Positions;
//var intensitis = segmentedScan.Intensities;
//Console.WriteLine(masses.Length);
//Console.WriteLine(intensitis.Length);
//Console.WriteLine(filterObj.MSOrder);
int cnt = 0;
while(cnt < scan.PreferredMasses.Length)
{
if(lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS )
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
writer.WriteLine("{0},{1},{2},{3},{4},{5},{6},{7}", startNum.ToString(), rt.ToString(),
msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(),
scanFilter.ToString(), levelInfo);
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getMSdataFromRT(double startRT, int endRT, string filePath, double lowMS = 0.00, double highMS = 0.00)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
plus.SelectInstrument(Device.MS, 1);
if (highMS - 0.00 <= 0.01)
{
highMS = plus.RunHeaderEx.HighMass;
}
int startNum = plus.ScanNumberFromRetentionTime(startRT);
int endNum = plus.ScanNumberFromRetentionTime(endRT);
int maxNum = plus.RunHeaderEx.LastSpectrum > endNum ? endNum : plus.RunHeaderEx.LastSpectrum;
string fileName = DateTime.Now.ToLocalTime().ToString().Replace("/", "").Replace(":", "").Replace(" ", "_") + ".csv";
FileStream stream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter writer = new StreamWriter(stream, Encoding.UTF8);
writer.WriteLine("ScanNumber, RT, Mass, Resolution, Intensity, Noise, Filter");
while (startNum <= endNum)
{
Scan scan = Scan.FromFile(plus, startNum);
string filter = plus.GetFilterForScanNumber(startNum).ToString();
int cnt = 0;
while (cnt < scan.PreferredMasses.Length)
{
if (lowMS < scan.PreferredMasses[cnt] && scan.PreferredMasses[cnt] < highMS)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
double msval = scan.PreferredMasses[cnt];
double resolution = (scan.PreferredResolutions.Length == 0) ? 0.0 : scan.PreferredResolutions[cnt];
double intensity = (scan.PreferredIntensities.Length == 0) ? 0.0 : scan.PreferredIntensities[cnt];
double noise = (scan.PreferredNoises.Length == 0) ? 0.0 : scan.PreferredNoises[cnt];
writer.WriteLine("{0},{1},{2},{3},{4},{5},{6}", startNum.ToString(), rt.ToString(), msval.ToString(), resolution.ToString(), intensity.ToString(), noise.ToString(), filter.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
