private void Window_Loaded(object sender, RoutedEventArgs e)
{
DataSetFactory.SearchFolder(".");
// read input data
var dataset = sds.DataSet.Open("Tutorial2.csv?inferDims=true&appendMetadata=true");
if (!dataset.Any(var => var.Name == "Model"))
{
var x = dataset.GetData <double[]>("X");
var y = dataset.GetData <double[]>("Observation");
// compute
var xm = x.Sum() / x.Length;
var ym = y.Sum() / y.Length;
double a = 0, d = 0;
for (int i = 0; i < x.Length; i++)
{
a += (x[i] - xm) * (y[i] - ym);
d += (x[i] - xm) * (x[i] - xm);
}
a /= d;
var b = ym - a * xm;
var model = x.Select(xx => a * xx + b).ToArray();
//
var varid = dataset.Add <double[]>("Model", dataset.Dimensions[0].Name).ID;
dataset.PutData <double[]>(varid, model);
}
Viewer.DataSet = dataset;
}
public MainWindow()
{
DataSetFactory.SearchFolder(Environment.CurrentDirectory);
InitializeComponent();
InitModel();
dsvc.DataSet = dataset;
}
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();
}
}
static void Main(string[] args)
{
if (args.Length == 0)
{
PrintUsage(); return;
}
#if DEBUG
Console.WriteLine("DEBUG version: searching current folder for providers...");
DataSetFactory.SearchFolder(".");
#endif
try
{
string command = args[0];
if (args.Length == 1 && (command.Contains('.') || command.Contains(':')))
{
// Command cannot . or : for these are mean either extension or schema prefix.
DoList(args[0]);
return;
}
if (command == "list")
{
if (!AssertNumberOfArgs(args, 2))
{
return;
}
DoList(args[1]);
}
else if (command == "meta")
{
if (!AssertNumberOfArgs(args, 2, int.MaxValue))
{
return;
}
DoMeta(args[1], GetCommandArgs(args, 2));
}
else if (command == "update")
{
if (!AssertNumberOfArgs(args, 4, int.MaxValue))
{
return;
}
DoUpdate(args[1], GetCommandArgs(args, 2));
}
else if (command == "data")
{
if (!AssertNumberOfArgs(args, 2, int.MaxValue))
{
return;
}
DoData(args[1], GetCommandArgs(args, 2));
}
else if (command == "copy")
{
if (!AssertNumberOfArgs(args, 3))
{
return;
}
DoCopy(args[1], args[2]);
}
else if (command == "info")
{
if (!AssertNumberOfArgs(args, 1))
{
return;
}
DoInfo();
}
else if (command == "/?" || command == "help")
{
PrintUsage();
}
else
{
WriteError("Unknown command.");
}
}
catch (Exception ex)
{
Console.ForegroundColor = ConsoleColor.Red;
Console.Write("\nFAILED: ");
do
{
#if DEBUG
Console.Error.WriteLine(ex);
#else
Console.Error.WriteLine(ex.Message);
#endif
ex = ex.InnerException;
} while (ex != null);
Console.ResetColor();
}
}
