private void ProcessRun(string folder_str)
{
if (string.IsNullOrWhiteSpace(folder_str))
{
MessageBox.Show("Path to folder should be specified!", "Folder path", MessageBoxButton.OK,
MessageBoxImage.Error);
return;
}
if (!Directory.Exists(folder_str))
{
Directory.CreateDirectory(folder_str);
}
var connStr = Settings.Default.ConnectionString;
if (string.IsNullOrWhiteSpace(connStr))
{
connStr = $"DSN=MonetDB;Host=scalpelhost;Port=50000;Database=msinvent;Uid=user;Pwd=password;";
}
var resultSpectrum = new List <object[]>();
var querySpectrum = $@"select distinct rtrim(t.label) || '-' || sm.label || '-' || s.id,
'Extraction',
'Melted samples in ' || sol.name,
'none',
'N/A',
'Chromatography',
'Mass spectrometry',
m.name,
r.min || '-' || r.max,
dev.name,
'MS:electrospray ionization',
sol.name,
res.name,
s.id,
p.sex,
p.yob,
d.name,
s.filename
from tissue t
inner join spectrum s on t.id = s.sampletumorid
INNER join patient p on p.id = t.patientid
inner join smpl sm on sm.id = s.sampleid
inner join device dev on dev.id = s.device
inner join mode m on m.id = s.mode
inner join mzrange r on r.id = s.mzrange
inner join solvent sol on sol.id = s.solvent
inner join resolution res on res.id = s.resolutionid
inner join diagnosis d on d.id = t.diagnosis
where s.ionsource < 5 and not t.label like ('%unspecified%');";
using (OdbcConnection con = new OdbcConnection(connStr))
{
con.Open();
using (OdbcCommand com = new OdbcCommand(querySpectrum, con))
{
using (OdbcDataReader reader = com.ExecuteReader())
{
while (reader.Read())
{
var result = new object[17];
var obj = reader.GetValues(result);
if (result[9].Equals("LTQ_Leninsky"))
{
result[9] = "MS:LTQ FT Ultra";
if (result[12].Equals("FT"))
{
result[11] = "MS:fourier transform ion cyclotron resonance mass spectrometer";
}
else
{
result[11] = "MS:linear ion trap";
}
}
else
{
result[9] = "MS:LTQ Orbitrap XL ETD";
if (result[12].Equals("FT"))
{
result[11] = "MS:orbitrap";
}
else
{
result[11] = "MS:linear ion trap";
}
}
resultSpectrum.Add(result);
}
}
foreach (object[] objects in resultSpectrum)
{
var spectrum = new MsSpectrum {
Id = (int)objects[13], RawFilePath = (string)objects[17]
};
var loggerStr = $"Processing spectrum, id = {spectrum.Id}";
logger.Info($"Processing spectrum, id = {spectrum.Id}");
Dispatcher.BeginInvoke(new Action(() =>
{
statusLabel.Content = loggerStr;
}), DispatcherPriority.Background);
Thread piThread = new Thread(() =>
{
try
{
SaveDataToCdf(spectrum, folder_str);
}
finally
{
spectrum = null;
}
})
{
IsBackground = true
};
piThread.Start();
}
}
}
var fstr = new StreamWriter(Path.Combine(folder_str, $"list.txt"));
foreach (var spectrum in resultSpectrum)
{
var line = new StringBuilder(String.Join(";", spectrum));
line.Append($";{Path.Combine(folder_str, $"{spectrum[13]}.cdf")}");
fstr.WriteLine(line.ToString());
}
fstr.Flush();
fstr.Close();
}
private void SaveDataToCdf(MsSpectrum spec, string fpath)
{
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.NetCDF4.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.Imperative.dll");
int nControllerType = 0; // 0 == mass spec device
int nContorllerNumber = 1; // first MS device
int totalNumScans = 0; // Number of scans
int firstScanNumber = 0, lastScanNumber = -1; // Number of first and last scan
string scanFilter = null; // Scan filter line
int numDataPoints = -1; // points in both the m/z and intensity arrays
double retentionTimeInMinutes = -1;
double minObservedMZ = -1;
double maxObservedMZ = -1;
double totalIonCurrent = -1;
double basePeakMZ = -1;
double basePeakIntensity = -1;
int channel = 0; // unused
int uniformTime = 0; // unused
double frequency = 0; // unused
int arraySize = -1;
object rawData = null; // rawData wil come as Double[,]
object peakFlags = null;
string szFilter = null; // No filter
int intensityCutoffType = 1; // No cutoff
int intensityCutoffValue = 0; // No cutoff
int maxNumberOfPeaks = 0; // 0 : return all data peaks
double centroidPeakWidth = 0; // No centroiding
int centroidThisScan = 0; // No centroiding
DateTime creationDate = DateTime.MinValue;
var scanPath = Path.Combine(fpath, $"{spec.Id}.cdf");
var cdf = DataSet.Open(scanPath);
cdf.IsAutocommitEnabled = false;
AddMetadata(cdf);
IXRawfile5 rawFile = (IXRawfile5) new MSFileReader_XRawfile();
rawFile.Open(spec.RawFilePath);
rawFile.SetCurrentController(nControllerType, nContorllerNumber);
rawFile.GetNumSpectra(ref totalNumScans);
rawFile.GetFirstSpectrumNumber(ref firstScanNumber);
rawFile.GetLastSpectrumNumber(ref lastScanNumber);
rawFile.GetCreationDate(ref creationDate);
var massVar = cdf.Add <double>("mass_values", new[] { "point_number" });
var intensities = cdf.Add <Int32>("intensity_values", new[] { "point_number" });
var acqTimeVar = cdf.Add <double>("scan_acquisition_time", new[] { "scan_number" });
var scIndexVar = cdf.Add <int>("scan_index", new[] { "scan_number" });
var scCountVar = cdf.Add <int>("point_count", new[] { "scan_number" });
var totalIntensityVar = cdf.Add <double>("total_intensity", new[] { "scan_number" });
massVar.Metadata["scale_factor"] = 1.0;
intensities.Metadata["scale_factor"] = 1.0;
try
{
var retTimes = new double[lastScanNumber];
var ticArr = new double[lastScanNumber];
var scanIndex = new Int32[lastScanNumber];
var pointCount = new Int32[lastScanNumber];
for (int curScanNum = firstScanNumber; curScanNum <= lastScanNumber; curScanNum++)
{
rawFile.GetScanHeaderInfoForScanNum(curScanNum,
ref numDataPoints,
ref retentionTimeInMinutes,
ref minObservedMZ,
ref maxObservedMZ,
ref totalIonCurrent,
ref basePeakMZ,
ref basePeakIntensity,
ref channel, // unused
ref uniformTime, // unused
ref frequency // unused
);
scanFilter = null;
rawFile.GetFilterForScanNum(curScanNum, ref scanFilter);
peakFlags = null;
centroidPeakWidth = 0;
arraySize = 0;
intensityCutoffType = 1;
intensityCutoffValue = (int)(0.001 * basePeakIntensity);
rawFile.GetMassListFromScanNum(
ref curScanNum,
szFilter, // filter
intensityCutoffType, // intensityCutoffType
intensityCutoffValue, // intensityCutoffValue
maxNumberOfPeaks, // maxNumberOfPeaks
centroidThisScan, // centroid result?
ref centroidPeakWidth, // centroidingPeakWidth
ref rawData, // daw data
ref peakFlags, // peakFlags
ref arraySize); // array size
;
var datArray = (Array)rawData;
var massArr = new double[arraySize];
var intArr = new int[arraySize];
for (var j = 0; j < arraySize; j++)
{
massArr[j] = (double)datArray.GetValue(0, j);
intArr[j] = Convert.ToInt32(datArray.GetValue(1, j));
}
//Console.Write($"curScan = {curScanNum}\n");
var ind = curScanNum - 1;
pointCount[ind] = arraySize;
if (ind == 0)
{
scanIndex[ind] = 0;
scanIndex[ind + 1] = arraySize;
}
else
{
scanIndex[ind] += scanIndex[ind - 1];
if (ind + 1 < lastScanNumber)
{
scanIndex[ind + 1] = arraySize;
}
}
retTimes[ind] = TimeSpan.FromMinutes(retentionTimeInMinutes).TotalSeconds;
ticArr[ind] = totalIonCurrent;
massVar.Append(massArr);
intensities.Append(intArr);
rawData = null;
}
totalIntensityVar.PutData(ticArr);
scIndexVar.PutData(scanIndex);
acqTimeVar.PutData(retTimes);
scCountVar.PutData(pointCount);
cdf.Commit();
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
finally
{
cdf.Dispose();
rawFile.Close();
}
}
