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);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="WiffExperiment"/> class
/// Base-Constructor. Performs the initalizations common to all experiments.
/// </summary>
/// <param name="msexperiment">Mass Spec Experiment</param>
/// <param name="wiffsample">Wiff Sample</param>
protected WiffExperiment(MSExperiment msexperiment, WiffSample wiffsample)
{
if (msexperiment == null)
{
throw new ArgumentNullException("msexperiment");
}
this.Init(msexperiment, wiffsample);
}
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));
}
}
}
}
}
/// <summary>
/// Determines with what kind of experiment we're dealing with and instatiates an object of the accurate
/// subclass derived from the abstract baseclass read the experiments properties and data.
/// WiffScanTypeEnumeration: Q1, MRM, SimQ1, Q3, SimQ3, Undefined, PrecursorIon, ProductIon, NeutralLoss, TofMS,
/// TofProductIon, TofPrecursorIon, EnhancedProductIon, EnhancedResolution, MS3, TimeDelayFragmentation, EnhancedMS, EnhancedMulticharge,
/// </summary>
/// <param name="msexperiment"> The msexperiment. </param>
/// <param name="wiffsample"> The wiffsample. </param>
/// <returns> The newly created, <see cref="WiffExperiment"/> dirived object. </returns>
public static WiffExperiment CreateWiffExperiment(MSExperiment msexperiment, WiffSample wiffsample)
{
ExperimentType expType = msexperiment.Details.ExperimentType;
WiffExperiment theExperiment;
switch (expType)
{
case ExperimentType.MRM:
{
theExperiment = new MrmScanExperiment(msexperiment, wiffsample);
}
break;
case ExperimentType.MS:
{
theExperiment = new MsScanExperiment(msexperiment, wiffsample);
}
break;
case ExperimentType.Precursor:
case ExperimentType.NeutralGainOrLoss:
case ExperimentType.Product:
case ExperimentType.SIM:
{
theExperiment = new MsScanExperiment(msexperiment, wiffsample);
}
break;
default:
{
// TODO -- Check if this is really, really intended...??
theExperiment = new MrmScanExperiment(msexperiment, wiffsample);
}
break;
}
return(theExperiment);
}
private static bool GetIsolationWindow(
MSExperiment exp,
out double isoWidth,
out double targetMz)
{
FragmentBasedScanMassRange mri = null;
MassRange[] mr = exp.Details.MassRangeInfo;
isoWidth = 0d;
targetMz = 0d;
if (mr.Length > 0)
{
mri = mr[0] as FragmentBasedScanMassRange;
isoWidth = mri.IsolationWindow * 0.5d;
targetMz = mri.FixedMasses[0];
}
return(mri != null);
}
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="inputMsExperiment"/>.
/// </summary>
/// <param name="inputMsExperiment">instance, the data source</param>
/// <param name="wiffsample"> Wiff Sample</param>
protected override void Initialize(MSExperiment inputMsExperiment, WiffSample wiffsample)
{
Cursor.Current = Cursors.WaitCursor;
try
{
// set the status information
AppContext.StatusInfo = "Getting wiff-data";
// (1) Get Maldi Parameters
string strMaldiParams = wiffsample.MaldiParametersString;
// (2) get the number of mass MRM transitions
this.massRanges = inputMsExperiment.Details.MassRangeInfo.Length;
// (3) select 1. MRM trace
XYData tic = inputMsExperiment.GetTotalIonChromatogram();
// (4) Dimension the data arrray, the number "data points"
this.numDataPoint = tic.NumDataPoints;
// (5) Set up arrays for info
this.rawData = new float[this.massRanges, this.numDataPoint];
this.timeData = new float[this.numDataPoint];
this.dwellTime = new double[this.massRanges];
this.massRangeName = new string[this.massRanges];
this.massRangeMax = new double[this.massRanges];
this.massRangeMin = new double[this.massRanges];
this.meanValues = new float[this.massRanges];
this.medianValues = new float[this.massRanges];
// helper for mean and median
var valuesForMedian = new List <float>();
// (6) loop through the mass ranges
for (int actMassRange = 0; actMassRange < this.massRanges; actMassRange++)
{
// get mass range object
this.massRangeName[actMassRange] = inputMsExperiment.Details.MassRangeInfo[actMassRange].Name;
this.dwellTime[actMassRange] = inputMsExperiment.Details.MassRangeInfo[actMassRange].DwellTime;
// loop through the spectrum
this.massRangeMax[actMassRange] = double.MinValue;
this.massRangeMin[actMassRange] = double.MaxValue;
double meanSum = 0.0;
valuesForMedian.Clear();
// Extract xic Full Scan
var option = new ExtractedIonChromatogramSettings(actMassRange);
ExtractedIonChromatogram xic = inputMsExperiment.GetExtractedIonChromatogram(option);
// JP 23/11 I think there might be a better way to do this.
for (int actDataPoint = 0; actDataPoint < this.numDataPoint; actDataPoint++)
{
// get the actual value
double anaXValue = xic.GetActualXValues()[actDataPoint];
double anaYValue = xic.GetActualYValues()[actDataPoint];
if (anaYValue < this.massRangeMin[actMassRange])
{
this.massRangeMin[actMassRange] = anaYValue;
}
if (anaYValue > this.massRangeMax[actMassRange])
{
this.massRangeMax[actMassRange] = anaYValue;
}
// now get the actual data
this.rawData[actMassRange, actDataPoint] = (float)anaYValue;
this.timeData[actDataPoint] = (float)anaXValue * 60;
// mean and median calculation...sum up the value to calculate the mean
meanSum += anaYValue;
// fill an extra array to calculate the median
valuesForMedian.Add((float)anaYValue);
}
// calculate the mean
this.meanValues[actMassRange] = (float)(meanSum / this.numDataPoint);
// calculate the median
valuesForMedian.Sort();
this.medianValues[actMassRange] = ((valuesForMedian.Count % 2) == 0) ? (valuesForMedian[(valuesForMedian.Count / 2) - 1] + valuesForMedian[valuesForMedian.Count / 2]) / 2.0f : valuesForMedian[valuesForMedian.Count / 2];
}
// (7) time per point in sec
this.timeinXDirection = (float)((tic.GetActualXValues()[this.numDataPoint - 1] - tic.GetActualXValues()[1]) * 60 / (this.numDataPoint - 2));
// (8) Calculate distInXDirection: fetch the x1, x2, y1, y2, width and height from the WiffSample instance this experiment belongs to.
double x1 = wiffsample.P1.X;
double y2 = 82 - wiffsample.P1.Y;
double x2 = wiffsample.P2.X;
double width = wiffsample.Width;
// (9) fetch the position data from the WiffSample instance this experiment belongs to.
uint[,] posData = wiffsample.PositionData;
long posDataLength = wiffsample.PositionDataLength;
// try and find the first and last valid indices in the posData, where valid means a nonzero time value...
long firstNonZeroTimeInPos = -1;
for (long t = 0; t < posDataLength - 1; t++)
{
if (posData[t, 0] > 0)
{
firstNonZeroTimeInPos = t + 1;
break; // ok, we're done...
}
}
long lastNonZeroTimeInPos = -1;
for (long t = posDataLength - 1; t >= 0; t++)
{
if (posData[t, 0] > 0)
{
lastNonZeroTimeInPos = t - 1;
break; // ok, we're done...
}
}
// (10) Make sure we have found valid values, bail out if not
if (firstNonZeroTimeInPos < 0 || lastNonZeroTimeInPos < 0)
{
// haven't found a valid posData triplet. All time values are zero or less...bail out
return;
}
// (11) Calculate distInYDirection
this.distInYDirection = 0;
for (long t = firstNonZeroTimeInPos; t < lastNonZeroTimeInPos; t++)
{
if ((posData[t, 1] > ((x2 + x1) * 500)) & Equals(this.distInYDirection, 0.0))
{
this.distInYDirection = posData[t, 2];
}
if ((posData[t, 1] < ((x2 + x1) * 500)) & (this.distInYDirection > 0))
{
this.distInYDirection = (float)Math.Round((decimal)(posData[t, 2] - this.distInYDirection) / 500, (int)(1 - Math.Log10((posData[t, 2] - this.distInYDirection) / 500))) / 2;
break;
}
}
// (12) Calculate speed in x direction
this.speedinXDirection = (float)Math.Round((posData[firstNonZeroTimeInPos + 2, 1] - posData[firstNonZeroTimeInPos + 1, 1]) / (decimal)(posData[firstNonZeroTimeInPos + 2, 0] - posData[firstNonZeroTimeInPos + 1, 0]) * 2, 0) / 2;
// (13) distInXDirection
this.distInXDirection = (float)(int)(this.speedinXDirection * this.timeinXDirection * 1000) / 1000;
// (14) number of points in x
this.numPointsOnXAxis = (int)(width / this.speedinXDirection / this.timeinXDirection);
// (15) number of points in y
// y2 from the wiff file is not the actual y2 from the stage - replace with value from path file...
// JP added "82 -" so what we convert wiff format to analyse co-ordinate system
var y1 = 82 - (double)Math.Round((decimal)posData[lastNonZeroTimeInPos, 2] / 1000, 2);
// ...and this has an effect of the numPointsOnYAxis
this.numPointsOnYAxis = (int)Math.Round((decimal)((y2 - y1) / this.distInYDirection) + 1);
// (16) Calc Lines Breaks
double syncTime1 = (float)posData[firstNonZeroTimeInPos, 0] / 1000;
double syncTime2 = (float)posData[lastNonZeroTimeInPos, 0] / 1000;
if (this.numPointsOnYAxis % 2 == 0)
{
// even number of scanlines
this.lineBreak = ((syncTime2 - syncTime1)
- ((x2 - ((float)posData[firstNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection)
- (((this.numPointsOnYAxis - 2) * (x2 - x1)) / this.speedinXDirection)
- ((x2 - ((float)posData[lastNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection))
/ (this.numPointsOnYAxis - 1);
}
else
{
// odd number of scanlines
this.lineBreak = ((syncTime2 - syncTime1)
- ((x2 - ((float)posData[firstNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection)
- (((this.numPointsOnYAxis - 2) * (x2 - x1)) / this.speedinXDirection)
- ((((float)posData[lastNonZeroTimeInPos, 1] / 1000) - x1) / this.speedinXDirection))
/ (this.numPointsOnYAxis - 1);
}
// (17) time offset
this.timeOffset = ((float)posData[firstNonZeroTimeInPos, 0] / 1000) - ((((float)posData[firstNonZeroTimeInPos, 1] / 1000) - x1) / this.speedinXDirection);
double dwellTimeSum = 0;
AppContext.StatusInfo = string.Empty;
// (18) Format Data
for (int actMassRange = 0; actMassRange < this.massRanges; actMassRange++)
{
// format the data into a rectangular, 2 dimensional array of floats that will represent the image data
var imageData = new float[this.numPointsOnXAxis][];
for (int i = 0; i < imageData.Length; i++)
{
imageData[i] = new float[this.numPointsOnYAxis];
}
dwellTimeSum -= this.dwellTime[actMassRange] / 1000 / 2;
double optTimeOffset = this.timeOffset;
double optLineBreak = this.lineBreak;
if (AppContext.UseApproximation)
{
// Perform the optimization...
this.HeuristicOptimization(imageData, actMassRange, x2 - x1, dwellTimeSum, ref optLineBreak, ref optTimeOffset);
}
this.FormatImageSharp(imageData, actMassRange, x2 - x1, dwellTimeSum, optLineBreak, optTimeOffset);
dwellTimeSum -= this.dwellTime[actMassRange] / 1000 / 2;
// create the appropriate dataset and add it to the WiffFileContent object...
string imgName = wiffsample.Name + " : " + this.massRangeName[actMassRange];
Document doc = wiffsample.WiffFileContent.Document;
// create the meta information data structure and populate with relevant information...
var metaData = new ImageMetaData();
try
{
const float Epsilon = (float)1E-10;
metaData.Add("Sample Name", typeof(string), wiffsample.Name, false);
metaData.Add("Mass Range", typeof(string), this.massRangeName[actMassRange], false);
metaData.Add("X1 (mm)", typeof(string), (Math.Abs(x1 - (int)x1) < Epsilon) ? x1.ToString("0.0") : x1.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Y1 (mm)", typeof(string), (Math.Abs(y1 - (int)y1) < Epsilon) ? y1.ToString("0.0") : y1.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("X2 (mm)", typeof(string), (Math.Abs(x2 - (int)x2) < Epsilon) ? x2.ToString("0.0") : x2.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Y2 (mm)", typeof(string), (Math.Abs(y2 - (int)y2) < Epsilon) ? y2.ToString("0.0") : y2.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Data Points in X", typeof(string), this.numPointsOnXAxis.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Data Points in Y", typeof(string), this.numPointsOnYAxis.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Point Width (mm)", typeof(string), Math.Round(this.distInXDirection, 2).ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Point Height (mm)", typeof(string), Math.Round(this.distInYDirection, 2).ToString(CultureInfo.InvariantCulture), false);
// Add Maldi Parameters
string[] splitstring = strMaldiParams.Split(SepMaldiParams, StringSplitOptions.None);
metaData.Add("Laser Frequency (Hz)", typeof(string), splitstring[1], false);
metaData.Add("Laser Power (%)", typeof(string), splitstring[2], false);
metaData.Add("Ablation Mode", typeof(string), splitstring[3], false);
metaData.Add("Skimmer Voltage (V)", typeof(string), splitstring[4], false);
metaData.Add("Source Gas", typeof(string), splitstring[5], false);
metaData.Add("Raster Speed (mm/s)", typeof(string), splitstring[6], false);
metaData.Add("Line Direction", typeof(string), splitstring[7], false);
metaData.Add("Rastor Pitch ", typeof(string), splitstring[8], false);
}
catch (Exception e)
{
Util.ReportException(e);
}
// (19) Create new ImageData and add WiffContent to Wiffsample
wiffsample.WiffFileContent.Add(new ImageData(
doc,
imageData,
imgName,
metaData,
(float)this.massRangeMin[actMassRange],
(float)this.massRangeMax[actMassRange],
this.meanValues[actMassRange],
this.medianValues[actMassRange],
(float)this.distInXDirection,
(float)this.distInYDirection,
null,
Core.ExperimentType.MRM));
}
}
finally
{
Cursor.Current = Cursors.Default;
}
}
/// <summary>
/// Initializes a new instance of the <see cref="MrmScanExperiment"/> class
/// </summary>
/// <param name="msexperiment">Mass Spec Experiment</param>
/// <param name="wiffsample">wiff sample</param>
public MrmScanExperiment(MSExperiment msexperiment, WiffSample wiffsample)
: base(msexperiment, wiffsample)
{
}
/// <summary>
/// Calls the virtual Initialize method
/// </summary>
/// <param name="msexperiment">Mass Spec Experiment</param>
/// <param name="wiffsample">Wiff Sample</param>
private void Init(MSExperiment msexperiment, WiffSample wiffsample)
{
this.Initialize(msexperiment, wiffsample);
}
/// <summary> /// Fills this instance data members with the information read from <paramref name="inputMsExperiment"/> /// </summary> /// <param name="inputMsExperiment">Mass Spec Experiment</param> /// <param name="wiffsample">Wiff Sample</param> protected abstract void Initialize(MSExperiment inputMsExperiment, WiffSample wiffsample);
/// <summary>
/// Fills this instance data members with the information read from <paramref name="inputMsExperiment"/>
/// </summary>
/// <param name="inputMsExperiment">Mass Spec Experiment</param>
/// <param name="wiffsample">Wiff Sample</param>
protected override void Initialize(MSExperiment inputMsExperiment, WiffSample wiffsample)
{
Cursor.Current = Cursors.WaitCursor;
try
{
// (1) Get Maldi Parameters
string strMaldiParams = wiffsample.MaldiParametersString;
this.msexperiment = inputMsExperiment;
// (2) Get the number of mass transitions - For MS experiments by default we will look at the first scan ([0])
MassRange massRange = this.msexperiment.Details.MassRangeInfo[0];
var fullScanMassRange = massRange as FullScanMassRange;
if (fullScanMassRange != null)
{
this.minMass = fullScanMassRange.StartMass;
this.maxMass = fullScanMassRange.EndMass;
this.massStepSize = fullScanMassRange.StepSize;
}
this.massSpecDataPoints = (int)(((this.maxMass - this.minMass) / this.massStepSize) + 1);
// (3) Populate masscal
this.masscal = new float[this.massSpecDataPoints];
for (int i = 0; i < this.massSpecDataPoints; i++)
{
this.masscal[i] = (float)(this.minMass + (i * this.massStepSize));
}
// (4) Select 1 trace
XYData tic = this.msexperiment.GetTotalIonChromatogram();
// (5) Dimension the data array, the number "data points"
this.numDataPoints = tic.NumDataPoints;
this.rawData = new float[this.numDataPoints];
this.timeData = new float[this.numDataPoints];
// (6) mass range info
this.massRangeName = "TIC " + this.msexperiment.Details.MassRangeInfo[0].Name;
double actualXValue = tic.GetActualXValues()[0];
this.massRangeMax = double.MinValue;
this.massRangeMin = double.MaxValue;
this.timeOffset = actualXValue * 1000;
// helper for mean and median
double meanSum = 0;
var valuesForMedian = new List <float>();
// (7) read the data...
for (int actDataPoint = 0; actDataPoint < this.numDataPoints; actDataPoint++)
{
// get the actual value...
actualXValue = tic.GetActualXValues()[actDataPoint];
double actualYValue = tic.GetActualYValues()[actDataPoint];
// and copy it to our local data structure
this.rawData[actDataPoint] = (float)actualYValue;
this.timeData[actDataPoint] = (float)actualXValue * 60;
// keep track of the extrema
if (actualYValue < this.massRangeMin)
{
this.massRangeMin = actualYValue;
}
if (actualYValue > this.massRangeMax)
{
this.massRangeMax = actualYValue;
}
// mean and median calculation... sum up the value to calculate the mean
meanSum += actualYValue;
// fill an extra array to calculate the median
valuesForMedian.Add((float)actualYValue);
}
// (8) Calculate the mean
this.meanValue = (float)(meanSum / this.numDataPoints);
// (9) Calculate the median
valuesForMedian.Sort();
this.medianValue = ((valuesForMedian.Count % 2) == 0) ? (valuesForMedian[(valuesForMedian.Count / 2) - 1] + valuesForMedian[valuesForMedian.Count / 2]) / 2.0f : valuesForMedian[valuesForMedian.Count / 2];
// (10) fetch the x1, x2, y1, y2, width and height from the WiffSample instance this experiment belongs to.
this.x1 = wiffsample.P1.X;
this.y2 = 82 - wiffsample.P1.Y;
this.x2 = wiffsample.P2.X;
this.width = wiffsample.Width;
// (11) time per point in s
this.timeinXDirection = (float)((tic.GetActualXValues()[this.numDataPoints - 1] - tic.GetActualXValues()[1]) * 60 / (this.numDataPoints - 2));
// (12) fetch the position data from the WiffSample instance this experiment belongs to.
uint[,] posData = wiffsample.PositionData;
long posDataLength = wiffsample.PositionDataLength;
// try and find the first and last valid indices in the posData, where valid means a nonzero time value...
long firstNonZeroTimeInPos = -1;
for (long t = 0; t < posDataLength - 1; t++)
{
if (posData[t, 0] > 0)
{
firstNonZeroTimeInPos = t;
break;
}
}
long lastNonZeroTimeInPos = -1;
for (long t = posDataLength - 1; t >= 0; t++)
{
if (posData[t, 0] > 0)
{
lastNonZeroTimeInPos = t;
break;
}
}
if (firstNonZeroTimeInPos < 0 || lastNonZeroTimeInPos < 0)
{
// haven't found a valid posData triplet. All time values are zero or less... bail out (Put in an Error Message here?)
return;
}
// (13) Distance in Y direction
this.distInYDirection = 0;
for (long t = firstNonZeroTimeInPos; t < lastNonZeroTimeInPos; t++)
{
if ((posData[t, 1] > ((this.x2 + this.x1) * 500)) & Equals(this.distInYDirection, 0.0))
{
this.distInYDirection = posData[t, 2];
}
if ((posData[t, 1] < ((this.x2 + this.x1) * 500)) & (this.distInYDirection > 0))
{
this.distInYDirection = (float)Math.Round((decimal)(posData[t, 2] - this.distInYDirection) / 500, (int)(1 - Math.Log10((posData[t, 2] - this.distInYDirection) / 500))) / 2;
break;
}
}
// (14) calculate speed in x direction
this.speedinXDirection = (float)Math.Round(((posData[firstNonZeroTimeInPos + 2, 1] - posData[firstNonZeroTimeInPos + 1, 1]) / (decimal)(posData[firstNonZeroTimeInPos + 2, 0] - posData[firstNonZeroTimeInPos + 1, 0]) * 2), 0) / 2;
// (15) distInXDirection
this.distInXDirection = (float)(int)(this.speedinXDirection * this.timeinXDirection * 1000) / 1000;
// (16) number of points in x
this.numPointsOnXAxis = (int)(this.width / this.speedinXDirection / this.timeinXDirection);
// (17) number of points in y
// y1 from the wiff file is not the actual y1 from the stage - replace with value from path file...
this.y1 = 82 - (double)Math.Round(((decimal)posData[lastNonZeroTimeInPos, 2] / 1000), 2);
// ...and this has an effect of the ypoints
this.numPointsOnYAxis = (int)Math.Round((decimal)((this.y2 - this.y1) / this.distInYDirection) + 1);
// (18) calculate the line breaks
var timeSpanPos = (posData[lastNonZeroTimeInPos, 0] / 1000.0)
- (posData[firstNonZeroTimeInPos, 0] / 1000.0);
if (this.numPointsOnYAxis % 2 == 0)
{
// even number of scanlines
this.lineBreak = (timeSpanPos - ((this.x2 - ((float)posData[firstNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection)
- (((this.numPointsOnYAxis - 2) * this.width) / this.speedinXDirection)
- ((this.x2 - ((float)posData[lastNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection)) / (this.numPointsOnYAxis - 1);
}
else
{
// odd number of scanlines
this.lineBreak = (timeSpanPos - ((this.x2 - ((float)posData[firstNonZeroTimeInPos, 1] / 1000)) / this.speedinXDirection)
- (((this.numPointsOnYAxis - 2) * this.width) / this.speedinXDirection)
- ((((float)posData[lastNonZeroTimeInPos, 1] / 1000) - this.x1) / this.speedinXDirection)) / (this.numPointsOnYAxis - 1);
}
this.lineBreak = this.lineBreak / this.timeinXDirection;
this.timeOffset = ((float)posData[firstNonZeroTimeInPos, 0] / 1000)
- ((((float)posData[firstNonZeroTimeInPos, 1] / 1000) - this.x1) / this.speedinXDirection);
this.lineOffset = (5 - ((this.timeData[5] - this.timeOffset) / this.timeinXDirection)) + 1;
// TIC throughout the total massrange...
// format the data into a rectangular, 2 dimensional array of floats that will represent the image data
AppContext.ProgressStart("formatting image data...");
// (19) copy the data from wiff file datastream to the rectangular array. Take account of the line offset and the line break timings
float[][] dataTic;
try
{
dataTic = new float[this.numPointsOnXAxis][];
this.sampleDataPos = new int[this.numPointsOnXAxis][];
for (int i = 0; i < dataTic.Length; i++)
{
dataTic[i] = new float[this.numPointsOnYAxis];
this.sampleDataPos[i] = new int[this.numPointsOnYAxis];
}
for (int pointOnYAxis = 0; pointOnYAxis < this.numPointsOnYAxis; pointOnYAxis++)
{
// currentLine is the offset to the start of the current line in the linear datastream (rawData)
var currentLine = (int)Math.Floor(Math.Abs(this.lineOffset
+ (((((this.x2 - this.x1) / this.speedinXDirection) / this.timeinXDirection)
+ this.lineBreak) * pointOnYAxis)));
for (int pointOnXAxis = 0; pointOnXAxis < this.numPointsOnXAxis; pointOnXAxis++)
{
int currentPoint;
if (pointOnYAxis % 2 == 0)
{
// even y: scan direction: -->
currentPoint = currentLine + pointOnXAxis;
}
else
{
// odd y: scan direction: <--
currentPoint = currentLine + this.numPointsOnXAxis - 1 - pointOnXAxis;
}
if (currentPoint < this.numDataPoints)
{
dataTic[pointOnXAxis][this.numPointsOnYAxis - 1 - pointOnYAxis] = this.rawData[currentPoint];
// Add in a new array to save these dataPos. We can use them to get the scan number
// Scan number is the current point
this.sampleDataPos[pointOnXAxis][this.numPointsOnYAxis - 1 - pointOnYAxis] = currentPoint;
}
else
{
dataTic[pointOnXAxis][this.numPointsOnYAxis - 1 - pointOnYAxis] = 0;
this.sampleDataPos[pointOnXAxis][this.numPointsOnYAxis - 1 - pointOnYAxis] = 0;
}
}
AppContext.ProgressSetValue((100.0 * pointOnYAxis) / this.numPointsOnYAxis);
}
}
finally
{
AppContext.ProgressClear();
}
// (20) create the appropriate dataset and add it to the WiffFileContent object...
string imgName = wiffsample.Name + " : " + this.massRangeName;
Document doc = wiffsample.WiffFileContent.Document;
// (21) Calculate Bin Points
// Set a default bin size of 1 - Important it is set to 1 and not zero
this.binsize = 1;
this.GetBinSize(wiffsample.ScanFileSize, this.numPointsOnXAxis, this.numPointsOnYAxis);
// By default we set this to massSpecDataPoints
this.binnedmassSpecDataPoints = this.massSpecDataPoints;
if (this.binsize > 1)
{
this.binnedmassSpecDataPoints = this.massSpecDataPoints / this.binsize;
}
// create the meta information data structure and populate with relevant information...
var metaData = new ImageMetaData();
try
{
const float Epsilon = (float)1E-10;
metaData.Add("Sample Name", typeof(string), wiffsample.Name, false);
metaData.Add("Mass Range", typeof(string), this.massRangeName, false);
metaData.Add("Mass Step Size", typeof(string), this.massStepSize, false);
metaData.Add("X1 (mm)", typeof(string), (Math.Abs(this.x1 - (int)this.x1) < Epsilon) ? this.x1.ToString("0.0") : this.x1.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Y1 (mm)", typeof(string), (Math.Abs(this.y1 - (int)this.y1) < Epsilon) ? this.y1.ToString("0.0") : this.y1.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("X2 (mm)", typeof(string), (Math.Abs(this.x2 - (int)this.x2) < Epsilon) ? this.x2.ToString("0.0") : this.x2.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Y2 (mm)", typeof(string), (Math.Abs(this.y2 - (int)this.y2) < Epsilon) ? this.y2.ToString("0.0") : this.y2.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Data Points in X", typeof(string), this.numPointsOnXAxis.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Data Points in Y", typeof(string), this.numPointsOnYAxis.ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Point Width (mm)", typeof(string), Math.Round(this.distInXDirection, 2).ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Point Height (mm)", typeof(string), Math.Round(this.distInYDirection, 2).ToString(CultureInfo.InvariantCulture), false);
metaData.Add("Bin Size", typeof(string), this.binsize.ToString(CultureInfo.InvariantCulture), false);
// Add Maldi Parameters
string[] splitstring = strMaldiParams.Split(SepMaldiParams, StringSplitOptions.None);
metaData.Add("Laser Frequency (Hz)", typeof(string), splitstring[1], false);
metaData.Add("Laser Power (%)", typeof(string), splitstring[2], false);
metaData.Add("Ablation Mode", typeof(string), splitstring[3], false);
metaData.Add("Skimmer Voltage (V)", typeof(string), splitstring[4], false);
metaData.Add("Source Gas", typeof(string), splitstring[5], false);
metaData.Add("Raster Speed (mm/s)", typeof(string), splitstring[6], false);
metaData.Add("Line Direction", typeof(string), splitstring[7], false);
metaData.Add("Rastor Pitch ", typeof(string), splitstring[8], false);
}
catch (Exception e)
{
Util.ReportException(e);
}
// (22) Create the ImageData
var imageTic = new ImageData(
doc,
dataTic,
imgName,
metaData,
(float)this.massRangeMin,
(float)this.massRangeMax,
this.meanValue,
this.medianValue,
(float)this.distInXDirection,
(float)this.distInYDirection,
this.masscal,
Core.ExperimentType.MS);
// (23) Collate the Spectrum Data
List <ImageData> imageDataList = null;
try
{
// (24) Create a list of array's to hold the mass spec images (in effect a 3x3 array or a list of 2x2 array)
this.dataList = new List <float[][]>();
for (int numMassSpecDataPts = 0; numMassSpecDataPts < this.binnedmassSpecDataPoints; numMassSpecDataPts++)
{
var data = new float[this.numPointsOnXAxis][];
for (int pointOnXAxis = 0; pointOnXAxis < this.numPointsOnXAxis; pointOnXAxis++)
{
data[pointOnXAxis] = new float[this.numPointsOnYAxis];
}
this.dataList.Add(data);
}
// (25) Populate dataList. We can populate this by Scan (PopulateListByScan()) Or MassSpec (PopulateListByMass())
// For now we will use by Scan as it is more effcient
this.PopulateListByScan();
// (26) Create the list of imageData objects passed to the imageSpectrumData object on it's creation later on...
imageDataList = new List <ImageData>();
for (int massSpecDataPt = 0; massSpecDataPt < this.binnedmassSpecDataPoints; massSpecDataPt++)
{
float[][] specData = this.dataList[massSpecDataPt];
imgName = wiffsample.Name + " : " + this.massRangeName;
// TODO -- rethink if one should really calculate the mean, median, min, max etc. if the images aren't used for imaging but for export...
float minInt = float.MaxValue;
float maxInt = float.MinValue;
// helper for mean and median
meanSum = 0;
valuesForMedian.Clear();
{
for (int x = 0; x < this.numPointsOnXAxis; x++)
{
for (int y = 0; y < this.numPointsOnYAxis; y++)
{
float value = specData[x][y];
// keep track of the extrema
if (value < minInt)
{
minInt = value;
}
if (value > maxInt)
{
maxInt = value;
}
// mean and median calculation...
// sum up the value to calculate the mean
meanSum += value;
// fill an extra array to calculate the median
valuesForMedian.Add(value);
}
}
}
// calculate the mean
var mean = (float)(meanSum / (this.numPointsOnXAxis * this.numPointsOnYAxis));
// calculate the median
valuesForMedian.Sort();
float median = ((valuesForMedian.Count % 2) == 0)
? (valuesForMedian[(valuesForMedian.Count / 2) - 1]
+ valuesForMedian[valuesForMedian.Count / 2]) / 2.0f
: valuesForMedian[valuesForMedian.Count / 2];
// ok, now create the imageData and add to list...
var imageData = new ImageData(
doc,
specData,
imgName,
metaData,
minInt,
maxInt,
mean,
median,
(float)this.distInXDirection,
(float)this.distInYDirection,
this.masscal,
Core.ExperimentType.MS);
imageDataList.Add(imageData);
}
}
catch (Exception e)
{
Util.ReportException(e);
}
// (27) Now everything should be set to create the ImageSpectrumData object...
imgName = wiffsample.Name + " SPECT " + this.massRangeMin.ToString(CultureInfo.InvariantCulture) + " - " + this.massRangeMax.ToString(CultureInfo.InvariantCulture);
var imageSpectrum = new ImageSpectrumData(
doc,
imgName,
metaData,
this.masscal,
imageDataList,
Core.ExperimentType.MS)
{
ImageTic = imageTic
};
wiffsample.WiffFileContent.Add(imageSpectrum);
}
finally
{
Cursor.Current = Cursors.Default;
}
}
/// <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);
}
}
public void SetActiveSample(int sampleIndex)
{
_activeSample = _wiffFile.GetSample(sampleIndex);
_activeMSExperiment = _activeSample.MassSpectrometerSample.GetMSExperiment(0);
}
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);
}
// 从sample中得到一个MSExperiment
public void GetMSExperiment(int experiment)
{
m_msExperiment = m_sample.MassSpectrometerSample.GetMSExperiment(experiment - 1);
}
public void SetActiveSample(int sampleIndex)
{
_activeSample = _wiffFile.GetSample(sampleIndex);
_activeMSExperiment = _activeSample.MassSpectrometerSample.GetMSExperiment(0);
}