public double GetFramePressureFront(int frameNum)
{
var fp = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameParams(frameNum);
var framepressureFront = fp.GetValueDouble(FrameParamKeyType.PressureFront);
return(framepressureFront);
}
public void GetFrameDataAllFrameSets()
{
Check.Require(ScanSetCollection != null && ScanSetCollection.ScanSetList.Count > 0, "Cannot get frame data. FrameSet collection has not been defined.");
Console.Write("Loading frame parameters ");
var dtLastProgress = DateTime.UtcNow;
if (ScanSetCollection == null)
{
return;
}
foreach (var scanSet in ScanSetCollection.ScanSetList)
{
var frame = (LCScanSetIMS)scanSet;
var fp = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFrameParams(frame.PrimaryScanNumber);
frame.AvgTOFLength = fp.GetValueDouble(FrameParamKeyType.AverageTOFLength);
frame.FramePressureUnsmoothed =
UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFramePressureForCalculationOfDriftTime(frame.PrimaryScanNumber);
if (DateTime.UtcNow.Subtract(dtLastProgress).TotalSeconds >= 1)
{
Console.Write(".");
dtLastProgress = DateTime.UtcNow;
}
}
Console.WriteLine();
}
public override double GetTime(int frameNum)
{
var fp = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFrameParams(frameNum);
var time = fp.GetValueDouble(FrameParamKeyType.StartTimeMinutes);
return(time);
}
public UIMFRun(string fileName)
: this()
{
Check.Require(File.Exists(fileName), "UIMF file does not exist.");
Filename = fileName;
_globalParams = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetGlobalParams();
Check.Ensure(_globalParams != null, "UIMF file's Global parameters could not be initialized. Check UIMF file to make sure it is a valid file.");
var baseFilename = Path.GetFileName(Filename);
if (baseFilename != null)
{
DatasetName = baseFilename.Substring(0, baseFilename.LastIndexOf('.'));
}
DataSetPath = Path.GetDirectoryName(fileName);
MinLCScan = GetMinPossibleLCScanNum();
MaxLCScan = GetMaxPossibleLCScanNum();
MinIMSScan = GetMinPossibleIMSScanNum();
MaxIMSScan = GetMaxPossibleIMSScanNum();
GetMSLevelInfo();
ContainsMSMSData = CheckRunForMSMSData();
}
/// <summary>
/// Returns the MSLevel for the given frame
/// </summary>
/// <param name="frameNum">Frame number</param>
/// <returns>1 for MS1 frames, 2 for MS2 frames, 0 for calibration frames, </returns>
public override int GetMSLevelFromRawData(int frameNum)
{
if (MS1Frames.BinarySearch(frameNum) >= 0)
{
return(1);
}
if (MS2Frames.BinarySearch(frameNum) >= 0)
{
return(2);
}
var fp = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFrameParams(frameNum);
if (fp.FrameType == DataReader.FrameType.MS1)
{
return(1);
}
if (fp.FrameType == DataReader.FrameType.MS2)
{
return(2);
}
if (fp.FrameType == DataReader.FrameType.Calibration)
{
return(0);
}
return(1);
}
/// <summary>
/// The total number of frames in the run
/// </summary>
/// <returns></returns>
public int GetNumFrames()
{
if (_globalParams == null)
{
_globalParams = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetGlobalParams();
}
return(_globalParams.NumFrames);
}
public override void Close()
{
if (UIMFLibraryAdapter.getInstance(this.Filename).Datareader != null)
{
UIMFLibraryAdapter.getInstance(this.Filename).CloseCurrentUIMF();
}
base.Close();
}
internal int GetNumScansPerFrame()
{
//TODO: check this and make sure it is correct
var minFrame = MinLCScan;
var numScansPerFrame = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameParams(minFrame).Scans;
return(numScansPerFrame);
}
public override int GetNumMSScans()
{
var numFrames = _globalParams.NumFrames;
var frameParams = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameParams(1);
var numScansPerFrame = frameParams.Scans;
return(numScansPerFrame * numFrames);
}
/// <summary>
/// Returns the mass spectrum for a specified LC Scanset and a IMS Scanset.
/// </summary>
/// <param name="lcScanset"></param>
/// <param name="imsScanset"></param>
/// <param name="minMZ"></param>
/// <param name="maxMZ"></param>
public override XYData GetMassSpectrum(ScanSet lcScanset, ScanSet imsScanset, double minMZ, double maxMZ)
{
Check.Require(imsScanset.GetScanCount() > 0, "Cannot get spectrum. Number of scans in ScanSet is 0");
Check.Require(lcScanset.GetScanCount() > 0, "Cannot get spectrum. Number of frames in FrameSet is 0");
var frameLower = lcScanset.getLowestScanNumber();
var frameUpper = lcScanset.getHighestScanNumber();
var scanLower = imsScanset.getLowestScanNumber();
var scanUpper = imsScanset.getHighestScanNumber();
// TODO: If lowest and highest scan numbers are both 0, should we be summing the mass spectrum?
var frameType = (DataReader.FrameType)GetMSLevel(lcScanset.PrimaryScanNumber);
try
{
// Obtain an instance of the reader
var uimfReader = UIMFLibraryAdapter.getInstance(Filename).Datareader;
// Prior to January 2015 the SpectrumCache class in the UIMFReader used Dictionary<int, int> for ListOfIntensityDictionaries
// This caused some datasets, e.g. EXP-Mix5_1um_pos_19Jan15_Columbia_DI, to run out of memory when caching 10 spectra
// The UIMFLibrary now uses List<int, int>, which takes up less memory (at the expense having slower lookups by BinNumber, though this does not affect DeconTools' use of the UIMFLibrry)
uimfReader.SpectraToCache = 10;
uimfReader.MaxSpectrumCacheMemoryMB = 750;
double[] xvals;
int[] yvals;
var nonZeroLength = uimfReader.GetSpectrum(frameLower,
frameUpper, frameType, scanLower, scanUpper, minMZ, maxMZ, out xvals, out yvals);
var xydata = new XYData();
if (xvals == null || xvals.Length == 0)
{
xydata.Xvalues = null;
xydata.Yvalues = null;
return(xydata);
}
xydata.Xvalues = xvals;
xydata.Yvalues = yvals.Select <int, double>(i => i).ToArray();
if (xydata.Xvalues[0] < minMZ || xydata.Xvalues[xydata.Xvalues.Length - 1] > maxMZ)
{
xydata = xydata.TrimData(minMZ, maxMZ);
}
return(xydata);
}
catch (Exception ex)
{
Console.WriteLine("Error in UIMF GetMassSpectrum: " + ex.Message);
throw;
}
}
public double GetFramePressure(int frameNum)
{
if (!this._framePressuresUnsmoothed.ContainsKey(frameNum))
{
var pressure = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFramePressureForCalculationOfDriftTime(frameNum);
this._framePressuresUnsmoothed.Add(frameNum, pressure);
}
return(this._framePressuresUnsmoothed[frameNum]);
}
public float GetTIC(int lcScan, int imsScan)
{
var frameScans = UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFrameScans(lcScan);
var query = (from item in frameScans where item.Scan == imsScan select item.TIC).ToList();
if (query.Count == 0)
{
return(0);
}
return((float)query.FirstOrDefault());
}
public double GetDriftTime(int frameNum, int scanNum)
{
var fp = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameParams(frameNum);
var avgTOFLength = fp.GetValueDouble(FrameParamKeyType.AverageTOFLength);
var driftTime = avgTOFLength * (scanNum + 1) / 1e6; //note that scanNum is zero-based. Need to add one here
var framePressure = GetFramePressure(frameNum);
if (Math.Abs(framePressure) > float.Epsilon)
{
driftTime = driftTime * (FramePressureStandard / framePressure); // correc
}
return(driftTime);
}
private void GetMSLevelInfo()
{
_frameList = new SortedDictionary <int, DataReader.FrameType>(UIMFLibraryAdapter.getInstance(Filename).Datareader.GetMasterFrameList());
MS1Frames = new List <int>();
MS2Frames = new List <int>();
var ms1Frames = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameNumbers(DataReader.FrameType.MS1);
if (ms1Frames != null && ms1Frames.Length != 0)
{
MS1Frames = ms1Frames.ToList();
}
var ms2Frames = UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameNumbers(DataReader.FrameType.MS2);
if (ms2Frames != null && ms2Frames.Length != 0)
{
MS2Frames = ms2Frames.ToList();
}
}
//public void GetDriftTimeProfile(int frameStartIndex, int frameStopIndex, int startScan, int stopScan, double targetMZ, double toleranceInMZ)
//{
// int[] scanValues = null;
// int[] intensityVals = null;
// UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetDriftTimeProfile(frameStartIndex, frameStopIndex, this.FrameTypeForMS1, startScan, stopScan, targetMZ, toleranceInMZ, ref scanValues, ref intensityVals);
// if (scanValues == null || scanValues.Length == 0)
// {
// this.XYData.Xvalues = null;
// this.XYData.Yvalues = null;
// }
// else
// {
// this.XYData.Xvalues = scanValues.Select<int, double>(i => i).ToArray();
// this.XYData.Yvalues = intensityVals.Select<int, double>(i => i).ToArray();
// }
//}
public XYData GetDriftTimeProfile(int frameNum, int startScan, int stopScan, double targetMZ, double toleranceInMZ)
{
int[] scanValues = null;
int[] intensityVals = null;
UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetDriftTimeProfile(frameNum, frameNum, DataReader.FrameType.MS1, startScan, stopScan, targetMZ, toleranceInMZ, ref scanValues, ref intensityVals);
var xydata = new XYData();
if (scanValues == null || scanValues.Length == 0)
{
xydata.Xvalues = null;
xydata.Yvalues = null;
}
else
{
xydata.Xvalues = scanValues.Select <int, double>(i => i).ToArray();
xydata.Yvalues = intensityVals.Select <int, double>(i => i).ToArray();
}
return(xydata);
}
//public int[][] GetFramesAndScanIntensitiesForAGivenMz(int startFrame, int endFrame, int frameType, int startScan, int endScan, double targetMz, double toleranceInMZ)
//{
// return UIMFLibraryAdapter.getInstance(this.Filename).Datareader.GetFramesAndScanIntensitiesForAGivenMz(startFrame, endFrame, frameType, startScan, endScan, targetMz, toleranceInMZ);
//}
////Anuj added this
//for now I am converting this dictionary to a frame and scna list, only because the UIMF library already has that method
//public void GetMassSpectrum(Dictionary<ushort, List<ushort>> frameAndScans, double minMz, double MaxMz)
//{
// List<ushort> frameNumbers = frameAndScans.Keys.ToList<ushort>();
// List<List<ushort>> scanNumbers = new List<List<ushort>>();
// foreach (ushort frameNum in frameNumbers)
// {
// List<ushort> scanList = frameAndScans[frameNum];
// scanNumbers.Add(scanList);
// }
// GetMassSpectrum(frameNumbers, scanNumbers, minMz, MaxMz);
//}
////Anuj added this
//public void GetMassSpectrum(List<ushort> frameNumbers, List<List<ushort>> scanNumbersForFrameNumbers, double minMz, double maxMz)
//{
// List<double> mzList = new List<double>();
// List<double> intensityList = new List<double>();
// UIMFLibraryAdapter.getInstance(this.Filename).Datareader.SumScansNonCached(frameNumbers, scanNumbersForFrameNumbers, mzList, intensityList, minMz, maxMz);
// this.XYData.Xvalues = mzList.ToArray();
// this.XYData.Yvalues = intensityList.ToArray();
//}
public Stack <int[]> GetDescendingBpiValuesByFramesAndScans()
{
return(UIMFLibraryAdapter.getInstance(Filename).Datareader.GetFrameAndScanListByDescendingIntensity());
}
