public static ScanEventReactionCollection ScanEvents(IRawDataPlus rawFile, ScanIndex index)
{
if (index.AnalysisOrder == MSOrderType.Ms)
{
Console.WriteLine("This is not an Orbitrap file. Skipping reaction event extraction.");
return(null);
}
else
{
rawFile.SelectMsData();
ScanEventReactionCollection events = new ScanEventReactionCollection();
Log.Information("Extracting scan events");
ProgressIndicator P = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Length, "Extracting reaction events");
P.Start();
foreach (int scan in index.ScanEnumerators[index.AnalysisOrder])
{
events.Add(scan, rawFile.GetScanEventForScanNumber(scan).GetReaction(0));
P.Update();
}
P.Done();
return(events);
}
}
public RawFileViz(string rawFile)
{
this.InitializeComponent();
#region initialize fields and containers
nextScanButton.Text = Char.ConvertFromUtf32(0x2192);
previousScanButton.Text = Char.ConvertFromUtf32(0x2190);
rawFileThreadManager = RawFileReaderFactory.CreateThreadManager(rawFile);
RawData = rawFileThreadManager.CreateThreadAccessor();
RawData.SelectMsData();
TotalNumScans = RawData.RunHeaderEx.SpectraCount;
FirstScan = RawData.RunHeader.FirstSpectrum;
LastScan = RawData.RunHeader.LastSpectrum;
currentScan = FirstScan;
TotalTime = RawData.RunHeader.EndTime;
this.Text = "ParseDataViz - " + RawData.FileName;
totalScansLabel.Text = String.Format("/ {0}", TotalNumScans);
splitContainer1.SplitterDistance = this.Size.Width - 300;
UpdateChromatogramData();
InitializeChromatogramPlot();
ChroMsLevelComboBox.SelectedIndex = 0;
initializeMassSpecData();
initializeMassSpectrum();
scanNumber.Text = FirstScan.ToString();
y = 0;
x = 1;
#endregion
//#region initial chromatogram
this.plotViewChromatogram.Model = chromatogram;
UpdateChromatogramPlot();
}
public static ScanEventReactionCollection ScanEvents(IRawDataPlus rawFile, ScanIndex index)
{
rawFile.SelectMsData();
ScanEventReactionCollection events = new ScanEventReactionCollection();
Log.Information("Extracting scan events");
ProgressIndicator P = new ProgressIndicator(index.ScanEnumerators[MSOrderType.Any].Length, "Extracting reaction events");
P.Start();
foreach (int scan in index.ScanEnumerators[index.AnalysisOrder])
{
events.Add(scan, rawFile.GetScanEventForScanNumber(scan).GetReaction(0));
P.Update();
}
P.Done();
return(events);
}
static int DoStuff(ArgumentParser.LogDumpOptions opts)
{
List <string> files = new List <string>();
if (opts.InputFiles.Count() > 0) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = opts.InputFiles.ToList();
// check if the list provided contains only .raw files
foreach (string file in files)
{
if (!file.EndsWith(".raw", StringComparison.OrdinalIgnoreCase))
{
problems.Add(file);
}
}
if (problems.Count() == 1)
{
Console.WriteLine("\nERROR: {0} does not appear to be a .raw file. Invoke '>RawTools --help' if you need help.", problems.ElementAt(0));
Log.Error("Invalid file provided: {0}", problems.ElementAt(0));
return(1);
}
if (problems.Count() > 1)
{
Console.WriteLine("\nERROR: The following {0} files do not appear to be .raw files. Invoke '>RawTools --help' if you need help." +
"\n\n{1}", problems.Count(), String.Join("\n", problems));
Log.Error("Invalid files provided: {0}", String.Join(" ", problems));
return(1);
}
Log.Information("Files to be processed, provided as list: {0}", String.Join(" ", files));
}
else // did the user give us a directory?
{
if (Directory.Exists(opts.InputDirectory))
{
files = Directory.GetFiles(opts.InputDirectory, "*.*", SearchOption.TopDirectoryOnly)
.Where(s => s.EndsWith(".raw", StringComparison.OrdinalIgnoreCase)).ToList();
}
else
{
Console.WriteLine("ERROR: The provided directory does not appear to be valid.");
Log.Error("Invalid directory provided: {0}", opts.InputDirectory);
return(1);
}
Log.Information("Files to be processed, provided as directory: {0}", String.Join(" ", files));
}
Console.WriteLine();
foreach (var file in files)
{
Console.WriteLine(Path.GetFileName(file));
Console.WriteLine("----------------------------------------");
using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(file))
{
rawFile.SelectMsData();
var numberOfLogs = rawFile.GetStatusLogEntriesCount();
var logInfo = rawFile.GetStatusLogHeaderInformation();
string logName = file + ".INST_LOG.txt";
Dictionary <int, ISingleValueStatusLog> log = new Dictionary <int, ISingleValueStatusLog>();
ProgressIndicator P = new ProgressIndicator(logInfo.Count(), "Preparing log data");
P.Start();
for (int i = 0; i < logInfo.Count(); i++)
{
log.Add(i, rawFile.GetStatusLogAtPosition(i));
P.Update();
}
P.Done();
using (StreamWriter f = new StreamWriter(logName))
{
P = new ProgressIndicator(numberOfLogs, $"Writing log");
P.Start();
f.Write("Time\t");
foreach (var x in logInfo)
{
f.Write(x.Label + "\t");
}
f.Write("\n");
for (int i = 0; i < numberOfLogs; i++)
{
f.Write($"{log[0].Times[i]}\t");
for (int j = 0; j < logInfo.Length; j++)
{
try
{
f.Write("{0}\t", log[j].Values[i]);
}
catch (Exception)
{
f.Write("\t");
}
}
f.Write("\n");
P.Update();
}
P.Done();
}
}
Console.WriteLine("\n");
}
return(0);
}
public static void WriteToDisk(WorkFlows.WorkflowParameters opts)
{
List <string> files = new List <string>();
Console.WriteLine();
Console.WriteLine("Writing log files");
foreach (var file in files)
{
Console.WriteLine(Path.GetFileName(file));
Console.WriteLine("----------------------------------------");
using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(file))
{
rawFile.SelectMsData();
var numberOfLogs = rawFile.GetStatusLogEntriesCount();
var logInfo = rawFile.GetStatusLogHeaderInformation();
string logName = file + ".INST_LOG.txt";
Dictionary <int, ISingleValueStatusLog> log = new Dictionary <int, ISingleValueStatusLog>();
ProgressIndicator P = new ProgressIndicator(logInfo.Count(), "Preparing log data");
P.Start();
for (int i = 0; i < logInfo.Count(); i++)
{
log.Add(i, rawFile.GetStatusLogAtPosition(i));
P.Update();
}
P.Done();
using (StreamWriter f = new StreamWriter(logName))
{
P = new ProgressIndicator(numberOfLogs, $"Writing log");
P.Start();
f.Write("Time\t");
foreach (var x in logInfo)
{
f.Write(x.Label + "\t");
}
f.Write("\n");
for (int i = 0; i < numberOfLogs; i++)
{
f.Write($"{log[0].Times[i]}\t");
for (int j = 0; j < logInfo.Length; j++)
{
try
{
f.Write("{0}\t", log[j].Values[i]);
}
catch (Exception)
{
f.Write("\t");
}
}
f.Write("\n");
P.Update();
}
P.Done();
}
}
Console.WriteLine("\n");
}
}