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");
}
}
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);
}
//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);
