/// <summary>
/// Initiates a dynamic connection with a Thermo .raw file. Data can be "streamed" instead of loaded all at once. Use
/// GetOneBasedScanFromDynamicConnection to get data from a particular scan. Use CloseDynamicConnection to close the
/// dynamic connection after all desired data has been retrieved from the dynamic connection.
/// </summary>
private void InitiateDynamicConnection(string filePath)
{
Loaders.LoadElements();
if (dynamicConnection != null)
{
dynamicConnection.Dispose();
}
dynamicConnection = RawFileReaderAdapter.FileFactory(filePath);
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
if (!dynamicConnection.IsOpen)
{
throw new MzLibException("Unable to access RAW file!");
}
if (dynamicConnection.IsError)
{
throw new MzLibException("Error opening RAW file!");
}
if (dynamicConnection.InAcquisition)
{
throw new MzLibException("RAW file still being acquired!");
}
dynamicConnection.SelectInstrument(Device.MS, 1);
GetMsOrdersByScanInDynamicConnection();
}
/// <summary>
/// Get and set general information from the raw file
/// </summary>
/// <param name="inputRawFile"></param>
/// <returns></returns>
private IRawDataPlus GetSetRawFileData(string inputRawFile)
{
// Create the IRawDataPlus object for accessing the RAW file
IRawDataPlus rawFile = RawFileReaderAdapter.FileFactory(inputRawFile);
if (!rawFile.IsOpen || rawFile.IsError)
{
Console.WriteLine("Unable to access the RAW file using the RawFileReader class!");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
Console.WriteLine("Error opening ({0})", rawFile.FileError);
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
Console.WriteLine("RAW file still being acquired...");
}
// Select instrument we are intereted in looking at data from
rawFile.SelectInstrument(Device.MS, 1);
return(rawFile);
}
/// <summary>
/// Open new Raw file with warning messages.
/// </summary>
/// <param name="path"></param>
public void Open(string path)
{
rawFile = RawFileReaderAdapter.FileFactory(path);
if (!rawFile.IsOpen)
{
Console.WriteLine(" RawFile Error: File could not be opened: " + path);
Console.WriteLine(rawFile.FileError.WarningMessage);
Console.WriteLine(rawFile.FileError.ErrorMessage);
Console.WriteLine(rawFile.FileError.ErrorCode);
throw new IOException("Failed to open RAW file.");
}
if (rawFile.IsError)
{
Console.WriteLine(" RawFile Error: reader error: " + path);
throw new IOException("Error while opening RAW file.");
}
rawFile.SelectInstrument(ThermoBiz.Device.MS, 1);
rawFile.IncludeReferenceAndExceptionData = true;
}
/// <summary>
/// Initiates a dynamic connection with a Thermo .raw file. Data can be "streamed" instead of loaded all at once. Use
/// GetOneBasedScanFromDynamicConnection to get data from a particular scan. Use CloseDynamicConnection to close the
/// dynamic connection after all desired data has been retrieved from the dynamic connection.
/// </summary>
protected override void InitiateDynamicConnection()
{
if (!File.Exists(FilePath))
{
throw new FileNotFoundException();
}
if (Path.GetExtension(FilePath).ToUpper() != ".RAW")
{
throw new InvalidDataException();
}
Loaders.LoadElements();
if (dynamicConnection != null)
{
dynamicConnection.Dispose();
}
dynamicConnection = RawFileReaderAdapter.FileFactory(FilePath);
if (!dynamicConnection.IsOpen)
{
throw new MzLibException("Unable to access RAW file!");
}
if (dynamicConnection.IsError)
{
throw new MzLibException("Error opening RAW file!");
}
if (dynamicConnection.InAcquisition)
{
throw new MzLibException("RAW file still being acquired!");
}
dynamicConnection.SelectInstrument(Device.MS, 1);
GetMsOrdersByScanInDynamicConnection();
}
public Rawfile(string rawfile)
{
int deviceNumber = 1;
_rawfile = rawfile;
rawFile = RawFileReaderAdapter.FileFactory(_rawfile);
// https://github.com/cpanse/MsBackendRawFileReader/issues/12
rawFile.IncludeReferenceAndExceptionData = false;
rawFile.SelectInstrument(Device.MS, deviceNumber);
dictInfo.Add("filename", rawFile.FileName);
dictInfo.Add("creation date", rawFile.FileHeader.CreationDate.ToString());
dictInfo.Add("first scan", this.GetFirstScanNumber().ToString());
dictInfo.Add("last scan", this.GetLastScanNumber().ToString());
dictInfo.Add("model", rawFile.GetInstrumentData().Model.ToString());
dictInfo.Add("name", rawFile.GetInstrumentData().Name.ToString());
dictInfo.Add("SerialNumber", rawFile.GetInstrumentData().SerialNumber.ToString());
//dictInfo.Add("mass resolution", rawFile.RunHeaderEx.MassResolution.ToString());
var trailerData = rawFile.GetTrailerExtraInformation(rawFile.RunHeaderEx.FirstSpectrum);
foreach (int i in Enumerable.Range(1, trailerData.Labels.ToArray().Length))
{
try
{
if ((trailerData.Labels[i] == "Master Scan Number:") ||
(trailerData.Labels[i] == "Master Scan Number") ||
(trailerData.Labels[i] == "Master Index:"))
{
this.masterScanIdx = i;
}
}
catch
{
}
}
}
/// <summary>
/// Loads all scan data from a Thermo .raw file.
/// </summary>
public static ThermoRawFileReader LoadAllStaticData(string filePath, IFilteringParams filterParams = null, int maxThreads = -1)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
Loaders.LoadElements();
// I don't know why this line needs to be here, but it does...
var temp = RawFileReaderAdapter.FileFactory(filePath);
var threadManager = RawFileReaderFactory.CreateThreadManager(filePath);
var rawFileAccessor = threadManager.CreateThreadAccessor();
if (!rawFileAccessor.IsOpen)
{
throw new MzLibException("Unable to access RAW file!");
}
if (rawFileAccessor.IsError)
{
throw new MzLibException("Error opening RAW file!");
}
if (rawFileAccessor.InAcquisition)
{
throw new MzLibException("RAW file still being acquired!");
}
rawFileAccessor.SelectInstrument(Device.MS, 1);
var msDataScans = new MsDataScan[rawFileAccessor.RunHeaderEx.LastSpectrum];
Parallel.ForEach(Partitioner.Create(0, msDataScans.Length), new ParallelOptions {
MaxDegreeOfParallelism = maxThreads
}, (fff, loopState) =>
{
IRawDataPlus myThreadDataReader = threadManager.CreateThreadAccessor();
myThreadDataReader.SelectInstrument(Device.MS, 1);
for (int s = fff.Item1; s < fff.Item2; s++)
{
try
{
var scan = GetOneBasedScan(myThreadDataReader, filterParams, s + 1);
msDataScans[s] = scan;
}
catch (Exception ex)
{
throw new MzLibException("Error reading scan " + (s + 1) + ": " + ex.Message);
}
}
});
rawFileAccessor.Dispose();
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
return(new ThermoRawFileReader(msDataScans, sourceFile));
}
private static void Main(string[] args)
{
// This local variable controls if the AnalyzeAllScans method is called
// bool analyzeScans = false;
const string rawR_version = "1.3.1";
string filename = string.Empty;
string mode = string.Empty;
string filterString = string.Empty;
Hashtable hashtable = new Hashtable()
{
{ "filter", "List all scan ids pass the filter string (option 2)." },
{ "getFilters", "List all scan filters of a given raw file." },
{ "isValidFilter", "Checks whether the provided argument string (option 2) is a valid filter." },
{ "headerR", "Writes the raw file's meta data as R code to a file." },
{ "chromatogram", "Extracts base peak and total ion count chromatograms into a file." },
{
"xic",
"Extracts filtered (option 2) ion chromatograms within a given mass and mass tolerance [in ppm] (option 3) xic of a given raw file as R code into a file."
},
{ "scans", "Extracts scans (spectra) of a given ID as Rcode." },
{ "cscans", "Extracts 'barbone' scans (spectra), including only mZ, intensity , precursorMass, rtinsecodonds and charge state, of a given ID as Rcode." },
{ "index", "Prints index as csv of all scans." }
};
var helpOptions = new List <string>()
{
"help", "--help", "-h", "h", "/h"
};
if (args.Length >= 2)
{
filename = args[0];
mode = args[1];
if (!hashtable.Contains(mode))
{
Console.WriteLine("\nOption '{0}' is not defined. Please use one of the following options as argument:", mode);
foreach (var k in hashtable.Keys)
{
Console.WriteLine(" {0,-15} {1}", k.ToString(), hashtable[k].ToString());
}
Console.WriteLine();
Environment.Exit(1);
}
}
else
{
if (args.Length == 0)
{
Console.WriteLine("No RAW file specified!");
return;
Console.WriteLine("run 'rawrr.exe help'.");
Environment.Exit(1);
}
else if (args[0] == "version")
{
Console.WriteLine(rawR_version);
Environment.Exit(0);
}
else if (helpOptions.Contains(args[0]))
{
Console.WriteLine("\nUsage:\n");
Console.WriteLine(" rawrr.exe <raw file> <option>\n");
Console.WriteLine(" rawrr.exe <raw file> <option> <input file> <output file>\n");
Console.WriteLine(
" rawrr.exe <raw file> <option 1> <option 2> <option 3> <input file> <output file>\n");
Console.WriteLine("\nOptions:\n");
foreach (var k in hashtable.Keys)
{
Console.WriteLine(" {0,-15} {1}", k.ToString(), hashtable[k].ToString());
}
Console.WriteLine("\nReport bugs at <https://github.com/fgcz/rawrr/issues>.\n");
Environment.Exit(0);
}
else
{
Console.WriteLine("run 'rawrr.exe help'.");
Environment.Exit(1);
}
}
if (string.IsNullOrEmpty(filename))
{
Console.WriteLine("No RAW file specified!");
return;
}
//Environment.Exit(0);
// Get the memory used at the beginning of processing
Process processBefore = Process.GetCurrentProcess();
long memoryBefore = processBefore.PrivateMemorySize64 / 1024;
try
{
// Create the IRawDataPlus object for accessing the RAW file
var rawFile = RawFileReaderAdapter.FileFactory(filename);
if (!rawFile.IsOpen || rawFile.IsError)
{
Console.WriteLine("Unable to access the RAW file using the RawFileReader class!");
return;
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
Console.WriteLine("Error opening ({0}) - {1}", rawFile.FileError, filename);
return;
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
Console.WriteLine("RAW file still being acquired - " + filename);
return;
}
rawFile.SelectInstrument(Device.MS, 1);
//Console.WriteLine("DEBUG {0}", rawFile.GetInstrumentMethod(3).ToString());
// Get the first and last scan from the RAW file
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
double startTime = rawFile.RunHeaderEx.StartTime;
double endTime = rawFile.RunHeaderEx.EndTime;
if (mode == "headerR")
{
var outputFilename = args[3];
rawFile.PrintHeaderAsRcode(outputFilename);
return;
}
// Get the number of filters present in the RAW file
int numberFilters = rawFile.GetFilters().Count;
if (mode == "filter")
{
filterString = args[2].ToString();
int precision = int.Parse(args[3]);
var outputFilename = args[4];
if (!IsValidFilter(rawFile, filterString))
{
Environment.Exit(1);
}
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(outputFilename))
{
foreach (var ss in rawFile
.GetFilteredScanEnumerator(rawFile.GetFilterFromString(filterString, precision)).ToArray())
{
file.WriteLine(ss);
}
}
Environment.Exit(0);
}
if (mode == "isValidFilter")
{
Console.WriteLine(IsValidFilter(rawFile, args[2].ToString()).ToString());
Environment.Exit(0);
}
if (mode == "getFilters")
{
foreach (var filter in rawFile.GetFilters())
{
Console.WriteLine(filter.ToString());
}
Environment.Exit(0);
}
if (mode == "version")
{
Console.WriteLine("version={}", rawR_version);
Environment.Exit(0);
}
if (mode == "chromatogram")
{
// Get the BasePeak chromatogram for the MS data
string filter = "ms";
string outputcsv = "chromatogram.csv";
try {
filter = args[2];
}
catch {
}
try {
outputcsv = args[3];
}
catch {
}
GetChromatogram(rawFile, firstScanNumber, lastScanNumber, outputcsv, filter);
Environment.Exit(0);
}
if (mode == "index")
{
rawFile.GetIndex();
return;
}
if (mode == "scans")
{
List <int> scans = new List <int>();
var scanfile = args[2];
int scanNumber;
foreach (var line in File.ReadAllLines(scanfile))
{
try{
Int32.TryParse(line, out scanNumber);
if (scanNumber > 0)
{
scans.Add(scanNumber);
}
}
catch {}
}
if (scans.Count == 0)
{
rawFile.WriteSpectrumAsRcode0(args[3]);
}
else
{
rawFile.WriteSpectrumAsRcode(args[3], scans);
}
return;
}
if (mode == "cscans")
{
List <int> scans = new List <int>();
var scanfile = args[2];
int scanNumber;
foreach (var line in File.ReadAllLines(scanfile))
{
try{
Int32.TryParse(line, out scanNumber);
if (scanNumber > 0)
{
scans.Add(scanNumber);
}
}
catch {}
}
if (scans.Count == 0)
{
rawFile.WriteSpectrumAsRcode0(args[3]);
}
else
{
rawFile.WriteCentroidSpectrumAsRcode(args[3], scans);
}
return;
}
if (mode == "xic")
{
// Console.WriteLine("xic");
try
{
double ppmError = Convert.ToDouble(args[2]);
// Console.WriteLine(ppmError);
string filter = "ms";
try {
filter = args[3];
}
catch {
}
//Console.WriteLine(filter);
var inputFilename = args[4];
var outputFilename = args[5];
List <double> massList = new List <double>();
if (File.Exists(inputFilename))
{
foreach (var line in File.ReadAllLines(inputFilename))
{
//Console.WriteLine(Convert.ToDouble(line));
massList.Add(Convert.ToDouble(line));
}
ExtractIonChromatogramAsRcode(rawFile, -1, -1, massList, ppmError, outputFilename, filter);
}
return;
}
catch (Exception ex)
{
Console.Error.WriteLine("failed to catch configfile and itol");
Console.Error.WriteLine("{}", ex.Message);
return;
}
}
}
catch (Exception ex)
{
Console.WriteLine("Error accessing RAWFileReader library! - " + ex.Message);
}
// Get the memory used at the end of processing
Process processAfter = Process.GetCurrentProcess();
long memoryAfter = processAfter.PrivateMemorySize64 / 1024;
Console.WriteLine();
Console.WriteLine("Memory Usage:");
Console.WriteLine(" Before {0} kb, After {1} kb, Extra {2} kb", memoryBefore, memoryAfter,
memoryAfter - memoryBefore);
}
private static void Main(string[] args)
{
// This local variable controls if the AnalyzeAllScans method is called
// bool analyzeScans = false;
string rawR_version = "0.0.1";
// Get the memory used at the beginning of processing
Process processBefore = Process.GetCurrentProcess();
long memoryBefore = processBefore.PrivateMemorySize64 / 1024;
try
{
// Check to see if the RAW file name was supplied as an argument to the program
string filename = string.Empty;
string mode = string.Empty;
Hashtable hashtable = new Hashtable()
{
{ "version", "print version information." },
{ "scanFilter", "print scan filters." },
{ "infoR", "print the raw file's meta data as R code." },
{ "chromatogram", "base peak chromatogram." },
{ "xic", "prints xic unfiltered." },
{ "tic", "prints xic unfiltered." },
{ "scans", "print spectrum of scanid as Rcode." },
{ "index", "print index as csv of all scans." }
};
if (args.Length > 0)
{
filename = args[0];
if (args.Length == 1)
{
Console.WriteLine("rawR version = {}", rawR_version);
Console.WriteLine("missing mode argument. setting to mode = 'info'.");
mode = "info";
}
else
{
mode = args[1];
}
if (!hashtable.Contains(mode))
{
Console.WriteLine("rawR version = {}", rawR_version);
Console.WriteLine("mode '{0}' not allowed. Please use one of the following modes:", mode);
foreach (var k in hashtable.Keys)
{
Console.WriteLine("{0} - {1}", k.ToString(), hashtable[k].ToString());
}
Environment.Exit(1);
}
}
if (string.IsNullOrEmpty(filename))
{
Console.WriteLine("No RAW file specified!");
return;
}
// Check to see if the specified RAW file exists
if (!File.Exists(filename))
{
Console.WriteLine("rawR version = {}", rawR_version);
Console.WriteLine(@"The file doesn't exist in the specified location - {0}", filename);
return;
}
// Create the IRawDataPlus object for accessing the RAW file
var rawFile = RawFileReaderAdapter.FileFactory(filename);
if (!rawFile.IsOpen || rawFile.IsError)
{
Console.WriteLine("Unable to access the RAW file using the RawFileReader class!");
return;
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
Console.WriteLine("Error opening ({0}) - {1}", rawFile.FileError, filename);
return;
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
Console.WriteLine("RAW file still being acquired - " + filename);
return;
}
rawFile.SelectInstrument(Device.MS, 1);
//Console.WriteLine("DEBUG {0}", rawFile.GetInstrumentMethod(3).ToString());
// Get the first and last scan from the RAW file
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
double startTime = rawFile.RunHeaderEx.StartTime;
double endTime = rawFile.RunHeaderEx.EndTime;
if (mode == "systeminfo")
{
Console.WriteLine("raw file name: {0}", Path.GetFileName(filename));
// Print some OS and other information
Console.WriteLine("System Information:");
Console.WriteLine(" OS Version: " + Environment.OSVersion);
Console.WriteLine(" 64 bit OS: " + Environment.Is64BitOperatingSystem);
Console.WriteLine(" Computer: " + Environment.MachineName);
Console.WriteLine(" number Cores: " + Environment.ProcessorCount);
Console.WriteLine(" Date: " + DateTime.Now);
}
if (mode == "infoR")
{
rawFile.PrintInfoAsRcode();
return;
}
// Display all of the trailer extra data fields present in the RAW file
// Get the number of filters present in the RAW file
int numberFilters = rawFile.GetFilters().Count;
// Get the scan filter for the first and last spectrum in the RAW file
//var firstFilter = rawFile.GetFilterForScanNumber(firstScanNumber);
//var lastFilter = rawFile.GetFilterForScanNumber(lastScanNumber);
if (mode == "scanFilter")
{
foreach (var filter in rawFile.GetFilters())
{
Console.WriteLine(filter.ToString());
}
Environment.Exit(0);
}
if (mode == "version")
{
Console.WriteLine("version={}", rawR_version);
Environment.Exit(0);
}
if (mode == "chromatogram")
{
// Get the BasePeak chromatogram for the MS data
string filter = "ms";
try {
filter = args[2];
}
catch {
}
GetChromatogram(rawFile, firstScanNumber, lastScanNumber, true, filter);
Environment.Exit(0);
}
if (mode == "index")
{
rawFile.GetIndex();
return;
}
if (mode == "scans")
{
List <int> scans = new List <int>();
var scanfile = args[2];
int scanNumber;
foreach (var line in File.ReadAllLines(scanfile))
{
try{
Int32.TryParse(line, out scanNumber);
if (scanNumber > 0)
{
scans.Add(scanNumber);
}
}
catch {}
}
if (scans.Count == 0)
{
rawFile.WriteSpectrumAsRcode0(args[3]);
}
else
{
rawFile.WriteSpectrumAsRcode(args[3], scans);
}
return;
}
if (mode == "xic")
{
try
{
var inputFilename = args[2];
double ppmError = Convert.ToDouble(args[3]);
var outputFilename = args[4];
string filter = "ms";
try {
filter = args[5];
}
catch {
}
List <double> massList = new List <double>();
if (File.Exists(args[2]))
{
foreach (var line in File.ReadAllLines(inputFilename))
{
massList.Add(Convert.ToDouble(line));
}
ExtractIonChromatogramAsRcode(rawFile, -1, -1, massList, ppmError, outputFilename, filter);
}
return;
}
catch (Exception ex)
{
Console.Error.WriteLine("failed to catch configfile and itol");
Console.Error.WriteLine("{}", ex.Message);
return;
}
}
}
catch (Exception ex)
{
Console.WriteLine("Error accessing RAWFileReader library! - " + ex.Message);
}
// Get the memory used at the end of processing
Process processAfter = Process.GetCurrentProcess();
long memoryAfter = processAfter.PrivateMemorySize64 / 1024;
Console.WriteLine();
Console.WriteLine("Memory Usage:");
Console.WriteLine(" Before {0} kb, After {1} kb, Extra {2} kb", memoryBefore, memoryAfter,
memoryAfter - memoryBefore);
}
//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);
//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);
//double[] masses = segmentedScan.Positions;
//double[] intensitis = segmentedScan.Intensities;
//Console.WriteLine(masses.Length);
//Console.WriteLine(intensitis.Length);
int cnt = 0;
if (scanFilter.MSOrder == MSOrderType.Ms)
{
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];
//msval.ToString("f4");Return a number to a given precision,carry bit
//msval.ToString("n4");Return a number to a given precision,not carry bit
//writer.WriteLine("{0},{1},{2},{3},{4},{5},{6},{7}", startNum.ToString(), rt.ToString(),
// msval.ToString("n4"), resolution.ToString(), intensity.ToString(), noise.ToString(),
// scanFilter.ToString(), levelInfo);
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
}
writer.Flush();
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());
}
}
writer.Flush();
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());
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getSRMIacdMZ(string filePath, double valMS,int recVal)
{
IRawDataPlus plus = RawFileReaderAdapter.FileFactory(filePath);
//////////////////////////////////
plus.SelectInstrument(Device.MS, 1);
/////////////////////////////////
var startNum = plus.RunHeaderEx.FirstSpectrum;
var 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);
double[] masses = null;
double[] intensities = null;
writer.WriteLine("ScanNumber, RT, Mass, Intensity");
while (startNum <= endNum)
{
double rt = plus.RetentionTimeFromScanNumber(startNum);
IScanFilter scanFilter = plus.GetFilterForScanNumber(startNum);
if (scanFilter.MSOrder == MSOrderType.Ms)
{
Scan scan = Scan.FromFile(plus, startNum);
IScanEvent scanEvent = plus.GetScanEventForScanNumber(startNum);
if (scan.HasCentroidStream && (scanEvent.ScanData == ScanDataType.Centroid || scanEvent.ScanData == ScanDataType.Profile))
{
var centroidStream = plus.GetCentroidStream(startNum, false);
if (scan.CentroidScan.Length > 0)
{
masses = centroidStream.Masses;
intensities = centroidStream.Intensities;
}
}
else
{
// Get the scan statistics from the RAW file for this scan number
var scanStatistics = plus.GetScanStatsForScanNumber(startNum);
// Get the segmented (low res and profile) scan data
var segmentedScan = plus.GetSegmentedScanFromScanNumber(startNum, scanStatistics);
if (segmentedScan.Positions.Length > 0)
{
masses = segmentedScan.Positions;
intensities = segmentedScan.Intensities;
}
}
for(int i = 0; i < masses.Length; ++ i)
{
masses[i] = Double.Parse(masses[i].ToString("n4"));
}
int front = 0;
int rear = masses.Length - 1;
int mid = front + ((rear - front) >> 1);
bool findVal = false;
while(front <= rear)
{
if (Double.Equals(masses[mid],valMS))
{
findVal = true;
break;
}
else if(masses[mid] < valMS)
{
front = mid + 1;
}
else
{
rear = mid - 1;
}
mid = front + ((rear - front) >> 1);
}
if(findVal && intensities[mid] >= recVal)
{
writer.WriteLine("{0},{1},{2},{3}",startNum.ToString(), rt.ToString(), masses[mid].ToString(), intensities[mid].ToString());
}
}
writer.Flush();
startNum += 1;
}
writer.Close();
}
}
}
}
}
writer.Flush();
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());
writer.WriteLine("{0},{1},{2},{3}", startNum.ToString(), rt.ToString(), msval.ToString(), intensity.ToString());
}
cnt += 1;
}
startNum += 1;
}
writer.Close();
}
public static void getSRMIacdMZ(string filePath, double valMS,int recVal)
//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();
}
private static void Main(string[] args)
{
// This local variable controls if the AnalyzeAllScans method is called
bool analyzeScans = false;
string rawDiagVersion = "0.0.35";
// Get the memory used at the beginning of processing
Process processBefore = Process.GetCurrentProcess();
long memoryBefore = processBefore.PrivateMemorySize64 / 1024;
try
{
// Check to see if the RAW file name was supplied as an argument to the program
string filename = string.Empty;
string mode = string.Empty;
Hashtable hashtable = new Hashtable()
{
{ "version", "print version information." },
{ "info", "print the raw file's meta data." },
{ "xic", "prints xic unfiltered." },
};
if (args.Length > 0)
{
filename = args[0];
if (args.Length == 1)
{
Console.WriteLine("rawDiag version = {}", rawDiagVersion);
Console.WriteLine("missing mode argument. setting to mode = 'info'.");
mode = "info";
}
else
{
mode = args[1];
}
if (!hashtable.Contains(mode))
{
Console.WriteLine("rawDiag version = {}", rawDiagVersion);
Console.WriteLine("mode '{0}' not allowed. Please use one of the following modes:", mode);
foreach (var k in hashtable.Keys)
{
Console.WriteLine("{0} - {1}", k.ToString(), hashtable[k].ToString());
}
Environment.Exit(1);
}
}
if (string.IsNullOrEmpty(filename))
{
Console.WriteLine("No RAW file specified!");
return;
}
// Check to see if the specified RAW file exists
if (!File.Exists(filename))
{
Console.WriteLine("rawDiag version = {}", rawDiagVersion);
Console.WriteLine(@"The file doesn't exist in the specified location - " + filename);
return;
}
// Create the IRawDataPlus object for accessing the RAW file
var rawFile = RawFileReaderAdapter.FileFactory(filename);
if (!rawFile.IsOpen || rawFile.IsError)
{
Console.WriteLine("Unable to access the RAW file using the RawFileReader class!");
return;
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
Console.WriteLine("Error opening ({0}) - {1}", rawFile.FileError, filename);
return;
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
Console.WriteLine("RAW file still being acquired - " + filename);
return;
}
if (mode == "info")
{
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
Console.WriteLine("Number of instruments: {0}", rawFile.InstrumentCount);
}
rawFile.SelectInstrument(Device.MS, 1);
//Console.WriteLine("DEBUG {0}", rawFile.GetInstrumentMethod(3).ToString());
// Get the first and last scan from the RAW file
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
double startTime = rawFile.RunHeaderEx.StartTime;
double endTime = rawFile.RunHeaderEx.EndTime;
if (mode == "systeminfo")
{
Console.WriteLine("raw file name: {0}", Path.GetFileName(filename));
// Print some OS and other information
Console.WriteLine("System Information:");
Console.WriteLine(" OS Version: " + Environment.OSVersion);
Console.WriteLine(" 64 bit OS: " + Environment.Is64BitOperatingSystem);
Console.WriteLine(" Computer: " + Environment.MachineName);
Console.WriteLine(" number Cores: " + Environment.ProcessorCount);
Console.WriteLine(" Date: " + DateTime.Now);
}
if (mode == "info")
{
// Get some information from the header portions of the RAW file and display that information.
// The information is general information pertaining to the RAW file.
Console.WriteLine("General File Information:");
Console.WriteLine(" RAW file: " + Path.GetFileName(rawFile.FileName));
Console.WriteLine(" RAW file version: " + rawFile.FileHeader.Revision);
Console.WriteLine(" Creation date: " + rawFile.FileHeader.CreationDate);
Console.WriteLine(" Operator: " + rawFile.FileHeader.WhoCreatedId);
Console.WriteLine(" Number of instruments: " + rawFile.InstrumentCount);
Console.WriteLine(" Description: " + rawFile.FileHeader.FileDescription);
Console.WriteLine(" Instrument model: " + rawFile.GetInstrumentData().Model);
Console.WriteLine(" Instrument name: " + rawFile.GetInstrumentData().Name);
// Console.WriteLine(" Instrument method: {0}", rawFile.GetAllInstrumentFriendlyNamesFromInstrumentMethod().Length);
Console.WriteLine(" Serial number: " + rawFile.GetInstrumentData().SerialNumber);
Console.WriteLine(" Software version: " + rawFile.GetInstrumentData().SoftwareVersion);
Console.WriteLine(" Firmware version: " + rawFile.GetInstrumentData().HardwareVersion);
Console.WriteLine(" Units: " + rawFile.GetInstrumentData().Units);
Console.WriteLine(" Mass resolution: {0:F3} ", rawFile.RunHeaderEx.MassResolution);
Console.WriteLine(" Number of scans: {0}", rawFile.RunHeaderEx.SpectraCount);
Console.WriteLine(" Number of ms2 scans: {0}",
Enumerable
.Range(1, lastScanNumber - firstScanNumber)
.Count(x => rawFile.GetFilterForScanNumber(x)
.ToString()
.Contains("Full ms2")));
Console.WriteLine(" Scan range: [{0}, {1}]", firstScanNumber, lastScanNumber);
Console.WriteLine(" Time range: [{0:F2}, {1:F2}]", startTime, endTime);
Console.WriteLine(" Mass range: [{0:F4}, {1:F4}]", rawFile.RunHeaderEx.LowMass,
rawFile.RunHeaderEx.HighMass);
Console.WriteLine();
// Get information related to the sample that was processed
Console.WriteLine("Sample Information:");
Console.WriteLine(" Sample name: " + rawFile.SampleInformation.SampleName);
Console.WriteLine(" Sample id: " + rawFile.SampleInformation.SampleId);
Console.WriteLine(" Sample type: " + rawFile.SampleInformation.SampleType);
Console.WriteLine(" Sample comment: " + rawFile.SampleInformation.Comment);
Console.WriteLine(" Sample vial: " + rawFile.SampleInformation.Vial);
Console.WriteLine(" Sample volume: " + rawFile.SampleInformation.SampleVolume);
Console.WriteLine(" Sample injection volume: " + rawFile.SampleInformation.InjectionVolume);
Console.WriteLine(" Sample row number: " + rawFile.SampleInformation.RowNumber);
Console.WriteLine(" Sample dilution factor: " + rawFile.SampleInformation.DilutionFactor);
Console.WriteLine();
// Read the first instrument method (most likely for the MS portion of the instrument).
// NOTE: This method reads the instrument methods from the RAW file but the underlying code
// uses some Microsoft code that hasn't been ported to Linux or MacOS. Therefore this
// method won't work on those platforms therefore the check for Windows.
if (Environment.OSVersion.ToString().Contains("Windows"))
{
var deviceNames = rawFile.GetAllInstrumentNamesFromInstrumentMethod();
foreach (var device in deviceNames)
{
Console.WriteLine("Instrument method: " + device);
}
Console.WriteLine();
}
}
// Display all of the trailer extra data fields present in the RAW file
// Get the number of filters present in the RAW file
int numberFilters = rawFile.GetFilters().Count;
// Get the scan filter for the first and last spectrum in the RAW file
var firstFilter = rawFile.GetFilterForScanNumber(firstScanNumber);
var lastFilter = rawFile.GetFilterForScanNumber(lastScanNumber);
if (mode == "info")
{
Console.WriteLine("Filter Information:");
Console.WriteLine(" Scan filter (first scan): " + firstFilter.ToString());
Console.WriteLine(" Scan filter (last scan): " + lastFilter.ToString());
Console.WriteLine(" Total number of filters: " + numberFilters);
Console.WriteLine();
// ListTrailerExtraFields(rawFile);
Environment.Exit(0);
}
if (mode == "version")
{
Console.WriteLine("version={}", rawDiagVersion);
Environment.Exit(0);
}
if (mode == "xic")
{
try
{
var inputFilename = args[2];
double ppmError = Convert.ToDouble(args[3]);
var outputFilename = args[4];
List <double> massList = new List <double>();
if (File.Exists(args[2]))
{
foreach (var line in File.ReadAllLines(inputFilename))
{
massList.Add(Convert.ToDouble(line));
}
GetXIC(rawFile, -1, -1, massList, ppmError, outputFilename);
}
return;
}
catch (Exception ex)
{
Console.Error.WriteLine("failed to catch configfile and itol");
Console.Error.WriteLine("{}", ex.Message);
return;
}
}
}
catch (Exception ex)
{
Console.WriteLine("Error accessing RAWFileReader library! - " + ex.Message);
}
// Get the memory used at the end of processing
Process processAfter = Process.GetCurrentProcess();
long memoryAfter = processAfter.PrivateMemorySize64 / 1024;
Console.WriteLine();
Console.WriteLine("Memory Usage:");
Console.WriteLine(" Before {0} kb, After {1} kb, Extra {2} kb", memoryBefore, memoryAfter,
memoryAfter - memoryBefore);
}