public Peak1DArray ReadSpectrumPeaks(string spectrumID)
{
RaiseDisposed();
try
{
int sampleIndex, experimentIndex, scanIndex;
Parse(spectrumID, out sampleIndex, out experimentIndex, out scanIndex);
using (MassSpectrometerSample sample = batch.GetSample(sampleIndex).MassSpectrometerSample)
using (MSExperiment msExp = sample.GetMSExperiment(experimentIndex))
{
Clearcore2.Data.MassSpectrum ms = msExp.GetMassSpectrum(scanIndex);
Peak1DArray pa = new Peak1DArray(
BinaryDataCompressionType.NoCompression,
BinaryDataType.Float32,
BinaryDataType.Float32);
//Peak1D[] peaks = new Peak1D[ms.NumDataPoints];
//for (int i = 0; i < ms.NumDataPoints; i++)
// peaks[i] = new Peak1D(ms.GetYValue(i), ms.GetXValue(i));
//pa.Peaks = MzLiteArray.ToMzLiteArray(peaks);
pa.Peaks = new WiffPeaksArray(ms);
return(pa);
}
}
catch (Exception ex)
{
throw new MzLiteIOException(ex.Message, ex);
}
}
public MzLiteModel CreateDefaultModel()
{
RaiseDisposed();
MzLiteModel model = new MzLiteModel(batch.Name);
string[] sampleNames = batch.GetSampleNames();
for (int sampleIdx = 0; sampleIdx < sampleNames.Length; sampleIdx++)
{
using (Clearcore2.Data.DataAccess.SampleData.Sample wiffSample = batch.GetSample(sampleIdx))
{
if (wiffSample.HasMassSpectrometerData)
{
string sampleName = sampleNames[sampleIdx].Trim();
string sampleID = ToRunID(sampleIdx);
MassSpectrometerSample msSample = wiffSample.MassSpectrometerSample;
MzLite.Model.Sample mzLiteSample = new MzLite.Model.Sample(
sampleID,
sampleName);
model.Samples.Add(mzLiteSample);
string softwareID = wiffSample.Details.SoftwareVersion.Trim();
Software software = null;
if (!model.Software.TryGetItemByKey(softwareID, out software))
{
software = new Software(softwareID);
model.Software.Add(software);
}
string instrumentID = msSample.InstrumentName.Trim();
Instrument instrument = null;
if (!model.Instruments.TryGetItemByKey(instrumentID, out instrument))
{
instrument = new Instrument(instrumentID);
instrument.Software = software;
model.Instruments.Add(instrument);
}
string runID = string.Format("sample={0}", sampleIdx);
Run run = new Run(runID);
run.Sample = mzLiteSample;
run.DefaultInstrument = instrument;
model.Runs.Add(run);
}
}
}
return(model);
}
private static IEnumerable <MzLite.Model.MassSpectrum> Yield(Batch batch, int sampleIndex)
{
using (MassSpectrometerSample sample = batch.GetSample(sampleIndex).MassSpectrometerSample)
{
for (int experimentIndex = 0; experimentIndex < sample.ExperimentCount; experimentIndex++)
{
using (MSExperiment msExp = sample.GetMSExperiment(experimentIndex))
{
for (int scanIndex = 0; scanIndex < msExp.Details.NumberOfScans; scanIndex++)
{
yield return(GetSpectrum(batch, sample, msExp, sampleIndex, experimentIndex, scanIndex));
}
}
}
}
}
public MzLite.Model.MassSpectrum ReadMassSpectrum(string spectrumID)
{
RaiseDisposed();
try
{
int sampleIndex, experimentIndex, scanIndex;
Parse(spectrumID, out sampleIndex, out experimentIndex, out scanIndex);
using (MassSpectrometerSample sample = batch.GetSample(sampleIndex).MassSpectrometerSample)
using (MSExperiment msExp = sample.GetMSExperiment(experimentIndex))
{
return(GetSpectrum(batch, sample, msExp, sampleIndex, experimentIndex, scanIndex));
}
}
catch (Exception ex)
{
throw new MzLiteIOException(ex.Message, ex);
}
}
/// <summary>
/// Fills this instance data members with the information read from <paramref name="wiffFile"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="Batch"/> instance. The data source.</param>
private void Initialize(Batch wiffFile)
{
Sample sample = wiffFile.GetSample(this.index);
// retrieve this sample's name
this.name = sample.Details.SampleName;
// get the position information for the selected sample the position data exists
// in a seperate file ( one per sample ) and is read from that file 'manually'
AppContext.ProgressStart("reading path file");
try
{
// 1) Set the various WiffSample Parameters
string pathFile = this.wiffFileContent.FileName + " (" + (this.index + 1).ToString(CultureInfo.InvariantCulture) + ").path";
// Make sure the path file exists
if (!File.Exists(pathFile))
{
MessageBox.Show(pathFile + " is missing", "Missing File");
return;
}
var positionStream = new FileStream(@pathFile, FileMode.Open, FileAccess.Read);
// calculate the count of position entries (12 bytes per position entry)
this.positionDataLength = positionStream.Length / 12;
this.x1 = 1e10;
this.x2 = 0.0;
this.y1 = 1e10;
this.y2 = 0.0;
// the array to hold the position information
this.positionData = new uint[this.positionDataLength, 3];
var positionReader = new BinaryReader(positionStream);
for (long posindex = 0; posindex < this.positionDataLength; posindex++)
{
this.positionData[posindex, 0] = positionReader.ReadUInt32();
this.positionData[posindex, 1] = positionReader.ReadUInt32();
this.positionData[posindex, 2] = positionReader.ReadUInt32();
// hundred progress ticks
if (Equals(posindex % (this.positionDataLength / 100.0), 0.0))
{
AppContext.ProgressSetValue(100.0 * posindex / this.positionDataLength);
}
if (this.positionData[posindex, 1] < this.x1)
{
this.x1 = this.positionData[posindex, 1];
}
if (this.positionData[posindex, 1] > this.x2)
{
this.x2 = this.positionData[posindex, 1];
}
if (this.positionData[posindex, 2] < this.y1)
{
this.y1 = this.positionData[posindex, 2];
}
if (this.positionData[posindex, 2] > this.y2)
{
this.y2 = this.positionData[posindex, 2];
}
}
positionReader.Close();
positionStream.Close();
this.x1 /= 1000;
this.x2 /= 1000;
this.y1 /= 1000;
this.y2 /= 1000;
this.width = this.x2 - this.x1;
this.height = this.y2 - this.y1;
}
finally
{
AppContext.ProgressClear();
}
// 2) Get the size of the scan file set scanfilesize
string scanpathFile = this.wiffFileContent.FileName + ".scan";
var fileinfo = new FileInfo(scanpathFile);
this.scanfilesize = fileinfo.Length;
MassSpectrometerSample massSpecSample = sample.MassSpectrometerSample;
int numberOfExperiments = massSpecSample.ExperimentCount;
// 3) Get number of experiments and create WiffExperiments for each
// loop through the experiments; the index of the experiments is zero based!!
for (int actExperiment = 0; actExperiment < numberOfExperiments; actExperiment++)
{
MSExperiment msexperiment = massSpecSample.GetMSExperiment(actExperiment);
WiffExperiment experiment = WiffExperimentFactory.CreateWiffExperiment(msexperiment, this);
this.experiments.Add(experiment);
}
}
private static MzLite.Model.MassSpectrum GetSpectrum(
Batch batch,
MassSpectrometerSample sample,
MSExperiment msExp,
int sampleIndex,
int experimentIndex,
int scanIndex)
{
MassSpectrumInfo wiffSpectrum = msExp.GetMassSpectrumInfo(scanIndex);
MzLite.Model.MassSpectrum mzLiteSpectrum = new Model.MassSpectrum(ToSpectrumID(sampleIndex, experimentIndex, scanIndex));
// spectrum
mzLiteSpectrum.SetMsLevel(wiffSpectrum.MSLevel);
if (wiffSpectrum.CentroidMode)
{
mzLiteSpectrum.SetCentroidSpectrum();
}
else
{
mzLiteSpectrum.SetProfileSpectrum();
}
// scan
Scan scan = new Scan();
scan.SetScanStartTime(wiffSpectrum.StartRT)
.UO_Minute();
mzLiteSpectrum.Scans.Add(scan);
// precursor
if (wiffSpectrum.IsProductSpectrum)
{
Precursor precursor = new Precursor();
double isoWidth;
double targetMz;
if (GetIsolationWindow(wiffSpectrum.Experiment, out isoWidth, out targetMz))
{
precursor.IsolationWindow
.SetIsolationWindowTargetMz(targetMz)
.SetIsolationWindowUpperOffset(isoWidth)
.SetIsolationWindowLowerOffset(isoWidth);
}
SelectedIon selectedIon = new SelectedIon();
selectedIon.SetSelectedIonMz(wiffSpectrum.ParentMZ)
.SetChargeState(wiffSpectrum.ParentChargeState);
precursor.SelectedIons.Add(selectedIon);
precursor.Activation
.SetCollisionEnergy(wiffSpectrum.CollisionEnergy);
mzLiteSpectrum.Precursors.Add(precursor);
}
return(mzLiteSpectrum);
}
