/// <summary>
/// The function gets the binsize
/// </summary>
/// <param name="scanfilesize">Size of the .scan file</param>
/// <param name="pointsInXDirection">Points in X Direction</param>
/// <param name="pointsInYDirection">Poitns in Y Direction</param>
private void GetBinSize(long scanfilesize, float pointsInXDirection, float pointsInYDirection)
{
// 1) We only want to do binning for files bigger than 100MB filesize > pathfilesize
string appPath = Application.StartupPath;
appPath += "\\ApplicationSettings.xml";
int filesizelimit = this.GetPathFileSizeLimit(appPath);
if (scanfilesize > filesizelimit)
{
// 2) Open up BinNumberWindow
MassRange massRange = this.msexperiment.Details.MassRangeInfo[0];
var fullScanMassRange = massRange as FullScanMassRange;
if (fullScanMassRange != null)
{
var binNumberWindow = new BinNumberWindow(pointsInXDirection, pointsInYDirection, this.masscal);
if (binNumberWindow.ShowDialog() == true)
{
if (binNumberWindow.BinSize > 0)
{
this.binsize = binNumberWindow.BinSize;
}
}
}
}
}
public double GetPrecusorMz(int spectrumNumber, double searchMZ, int msnOrder = 2)
{
int parentScanNumber = GetParentSpectrumNumber(spectrumNumber);
var ms1Scan = GetSpectrum(parentScanNumber);
MZPeak peak = ms1Scan.GetClosestPeak(MassRange.FromDa(searchMZ, 50));
if (peak != null)
{
return(peak.MZ);
}
return(double.NaN);
}
/// <summary>
/// Fills this instance data members with the information read from <paramref name="wiffFile"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The data source.</param>
protected override void Initialize(FMANWiffFileClass wiffFile)
{
// get experiment object and the experiment parameters
ITripleQuadMALDI experimentParams = (ITripleQuadMALDI)wiffFile.GetExperimentObject(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
Experiment experiment = (Experiment)wiffFile.GetExperimentObject(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
MassRange massRange = (MassRange)experiment.GetMassRange(0);
minMass = massRange.QstartMass; // anaSpec.GetStartMass();
maxMass = massRange.QstopMass; // anaSpec.GetStopMass();
massStepSize = massRange.QstepMass; //anaSpec.StepSize;
// get the number of MS data points
massSpecDataPoints = (int)((maxMass - minMass) / massStepSize + 1);
// select 1. data points
FMANChromData chrom = new FMANChromData();
chrom.WiffFileName = wiffFile.GetWiffFileName();
chrom.SetToTIC(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
// dimension the data arrray
nrDataPoints = chrom.GetNumberOfDataPoints();
rawData = new float[nrDataPoints];
timeData = new float[nrDataPoints];
//loop through the mass ranges
massRangeName = "TIC " + minMass.ToString() + " - " + maxMass.ToString();
double xValue = chrom.GetDataPointXValue(1);
double yValue = chrom.GetDataPointYValue(1);
massRangeMax = double.MinValue;
massRangeMin = double.MaxValue;
timeOffset = xValue * 1000;
// helper for mean and median
double meanSum = 0;
List <float> valuesForMedian = new List <float>();
// read the data...
for (int actDataPoint = 1; actDataPoint <= nrDataPoints; actDataPoint++)
{
// get the actual value...
xValue = chrom.GetDataPointXValue(actDataPoint);
yValue = chrom.GetDataPointYValue(actDataPoint);
// and copy it to our local data structur
rawData[actDataPoint - 1] = (float)yValue;
timeData[actDataPoint - 1] = (float)xValue * 60;
// keep track of the extrema
if (yValue < massRangeMin)
{
massRangeMin = yValue;
}
if (yValue > massRangeMax)
{
massRangeMax = yValue;
}
// mean and median calculation...
// sum up the value to calculate the mean
meanSum += yValue;
// fill an extra array to calculate the median
valuesForMedian.Add((float)yValue);
}
// calculate the mean
meanValue = (float)(meanSum / nrDataPoints);
// calculate the median
valuesForMedian.Sort();
medianValue = ((valuesForMedian.Count % 2) == 0) ? (float)(valuesForMedian[(valuesForMedian.Count / 2) - 1] + valuesForMedian[valuesForMedian.Count / 2]) / 2.0f : valuesForMedian[valuesForMedian.Count / 2];
#if (false) // analyze the timing values in timeData
List <float> timeSpans = new List <float>();
for (int i = 1; i < timeData.Length; i++)
{
timeSpans.Add(timeData[i] - timeData[i - 1]);
}
float tMean = 0;
float tMedian = 0;
timeSpans.Sort();
foreach (float ts in timeSpans)
{
tMean += ts;
}
tMean = tMean / timeSpans.Count;
tMedian = ((timeSpans.Count % 2) == 0) ? (float)(timeSpans[(timeSpans.Count / 2) - 1] + timeSpans[timeSpans.Count / 2]) / 2.0f : timeSpans[timeSpans.Count / 2];
#endif
// fetch the x1, x2, y1, y2, width and height from the WiffSample instance this experiment belongs to.
double x1 = WiffPeriod.Sample.P1.X;
double y1 = WiffPeriod.Sample.P1.Y;
double x2 = WiffPeriod.Sample.P2.X;
double y2 = WiffPeriod.Sample.P2.Y;
double width = WiffPeriod.Sample.Width;
double height = WiffPeriod.Sample.Height;
//get MALDI parmas and assign variables
string strMALDIParams = experimentParams.TripleQuadMALDIParameters;
// x speed in mm/s
xSpeed = float.Parse(strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None)[6]);
//line distance in mm
yDist = float.Parse(strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None)[8]) / 1000;
//time per point in s
xTime = (float)((chrom.GetDataPointXValue(nrDataPoints) - chrom.GetDataPointXValue(2)) * 60 / (nrDataPoints - 2));
xDist = (float)(int)(xSpeed * xTime * 1000) / 1000;
//number of poins in x
xPoints = (int)((width) / xSpeed / xTime);
// fetch the position data from the WiffSample instance this experiment belongs to.
uint[,] posData = WiffPeriod.Sample.PositionData;
long posDataLength = WiffPeriod.Sample.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;
// ok, we're done...
break;
}
}
long lastNonZeroTimeInPos = -1;
for (long t = posDataLength - 1; t >= 0; t++)
{
if (posData[t, 0] > 0)
{
lastNonZeroTimeInPos = t;
// ok, we're done...
break;
}
}
if (firstNonZeroTimeInPos < 0 || lastNonZeroTimeInPos < 0)
{
// haven't found a valid posData triplet. All time values are zero or less...
// bail out
return;
}
// y2 from the wiff file is not the actual y2 from the stage - replace with value from path file...
y2 = (double)Math.Round((decimal)posData[lastNonZeroTimeInPos, 2] / 1000, 2);
// ...and this has an effect of the ypoints
yPoints = (int)Math.Round((decimal)((y2 - y1) / yDist)) + 1;
double timeSpanPos = posData[lastNonZeroTimeInPos, 0] / 1000.0 - posData[firstNonZeroTimeInPos, 0] / 1000.0;
if (yPoints % 2 == 0)
{
// even number of scanlines
lineBreak = (timeSpanPos
- (x2 - (float)posData[firstNonZeroTimeInPos, 1] / 1000) / xSpeed
- (yPoints - 2) * (width) / xSpeed
- (x2 - (float)posData[lastNonZeroTimeInPos, 1] / 1000) / xSpeed)
/ (yPoints - 1);
}
else
{
// odd number of scanlines
lineBreak = (timeSpanPos
- (x2 - (float)posData[firstNonZeroTimeInPos, 1] / 1000) / xSpeed
- (yPoints - 2) * (width) / xSpeed
- ((float)posData[lastNonZeroTimeInPos, 1] / 1000 - x1) / xSpeed)
/ (yPoints - 1);
}
lineBreak = lineBreak / xTime;
timeOffset = (float)posData[firstNonZeroTimeInPos, 0] / 1000 - (((float)posData[firstNonZeroTimeInPos, 1] / 1000 - x1) / xSpeed);
lineOffset = (5 - (timeData[5] - timeOffset) / xTime) + 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("formating image data...");
// prepare the data structure
float[][] dataTIC;
try
{
dataTIC = new float[xPoints][];
for (int i = 0; i < dataTIC.Length; i++)
{
dataTIC[i] = new float[yPoints];
}
// copy the data from wiff file datastream to the rectangular array. Take account of the line offset and
// the line break timings.
for (int y = 0; y < yPoints; y++)
{
int currentPoint;
// currentLine is the offset to the start of the current line in the linear datastream (rawData)
int currentLine = (int)Math.Floor(Math.Abs(lineOffset + ((x2 - x1) / xSpeed / xTime + lineBreak) * y));
for (int x = 0; x < xPoints; x++)
{
if (y % 2 == 0)
{
// even y: scan direction: -->
currentPoint = (int)(currentLine + x);
}
else
{
// odd y: scan direction: <--
currentPoint = (int)(currentLine + xPoints - 1 - x);
}
if (currentPoint < nrDataPoints)
{
dataTIC[x][y] = rawData[currentPoint];
}
else
{
dataTIC[x][y] = 0;
}
}
AppContext.ProgressSetValue(100.0 * y / yPoints);
}
}
finally
{
AppContext.ProgressClear();
}
// create the appropriate dataset and add it to the WiffFileContent object...
string imgName = WiffPeriod.Sample.Name + " : " + massRangeName;
Document doc = WiffPeriod.Sample.WiffFileContent.Document;
//create the meta information data structure and populate with relevant information...
ImageMetaData metaData = new ImageMetaData();
try
{
metaData.Add("Sample Name", typeof(string), WiffPeriod.Sample.Name, false);
metaData.Add("Mass Range", typeof(string), massRangeName, false);
string[] splitted = strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None);
metaData.Add("Laser Frequency (Hz)", typeof(string), splitted[1], false);
metaData.Add("Laser Power (%)", typeof(string), splitted[2], false);
metaData.Add("Ablation Mode", typeof(string), splitted[3], false);
metaData.Add("Skimmer Voltage (V)", typeof(string), splitted[4], false);
metaData.Add("Source Gas", typeof(string), splitted[5], false);
metaData.Add("Raster Speed (mm/s)", typeof(string), splitted[6], false);
metaData.Add("Raster Pitch", typeof(string), splitted[8], false);
}
catch (Exception e) { Util.ReportException(e); }
ImageData imageTIC = new ImageData(doc, dataTIC, imgName, metaData, (float)massRangeMin, (float)massRangeMax,
(float)meanValue, (float)medianValue, (float)xDist, (float)yDist, (float)minMass, (float)maxMass);
///////////////////////////////////////////////////////////////////////////////////////////////////////
// Q1 spectrum scan...
FMANSpecData spec = new FMANSpecData();
spec.WiffFileName = wiffFile.GetWiffFileName();
// prepare the data structure
List <float[][]> dataList;
List <ImageData> imageDataList;
AppContext.ProgressStart("formating spectrum data...");
try
{
dataList = new List <float[][]>();
for (int i = 0; i < massSpecDataPoints; i++)
{
float[][] data = new float[xPoints][];
for (int j = 0; j < xPoints; j++)
{
data[j] = new float[yPoints];
}
dataList.Add(data);
}
for (int y = 0; y < yPoints; y++)
{
int currentPoint;
// currentLine is the offset to the start of the current line in the linear datastream (rawData)
int currentLine = (int)Math.Floor(Math.Abs(lineOffset + ((x2 - x1) / xSpeed / xTime + lineBreak) * y));
for (int x = 0; x < xPoints; x++)
{
if (y % 2 == 0)
{
// even y: scan direction: -->
currentPoint = (int)(currentLine + x);
}
else
{
// odd y: scan direction: <--
currentPoint = (int)(currentLine + xPoints - 1 - x);
}
if (currentPoint >= nrDataPoints)
{
continue;
}
float currentTime = (float)chrom.GetXValueInSec(currentPoint + 1);
spec.SetSpectrum(WiffPeriod.Sample.Index, WiffPeriod.Index, Index, currentTime, currentTime);
int specDataPoints = spec.GetNumberOfDataPoints();
for (int k = 1; k <= specDataPoints; k++)
{
int specIndex = (int)((spec.GetDataPointXValue(k) - minMass) / massStepSize + 0.4);
dataList[specIndex][x][y] = (float)spec.GetDataPointYValue(k);
}
}
AppContext.ProgressSetValue(100.0 * y / yPoints);
}
// create the list of imageData objects passed to the imageSpectrumData object on it's creation later on...
imageDataList = new List <ImageData>();
for (int k = 0; k < massSpecDataPoints; k++)
{
float[][] specData = dataList[k];
float mass = (float)(minMass + (massStepSize * k));
imgName = WiffPeriod.Sample.Name + " : " + mass.ToString();
// 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;
float mean = 0;
float median = 0;
// helper for mean and median
meanSum = 0;
valuesForMedian.Clear();
{
for (int x = 0; x < xPoints; x++)
{
for (int y = 0; y < yPoints; 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
mean = (float)(meanSum / (xPoints * yPoints));
// calculate the median
valuesForMedian.Sort();
median = ((valuesForMedian.Count % 2) == 0) ? (float)(valuesForMedian[(valuesForMedian.Count / 2) - 1] + valuesForMedian[valuesForMedian.Count / 2]) / 2.0f : valuesForMedian[valuesForMedian.Count / 2];
// ok, now create the imageData and add to list...
ImageData imageData = new ImageData(doc, specData, imgName, new ImageMetaData(), minInt, maxInt, mean, median, (float)xDist, (float)yDist, (float)0.0f, (float)mass);
imageDataList.Add(imageData);
}
}
finally
{
AppContext.ProgressClear();
}
// now everything should be set to create the ImageSpectrumData object...
imgName = WiffPeriod.Sample.Name + " SPECT " + minMass.ToString() + " - " + maxMass.ToString();
ImageSpectrumData imageSpectrum = new ImageSpectrumData(doc, imgName, new ImageMetaData(), imageDataList, (float)minMass, (float)maxMass, (float)massStepSize);
imageSpectrum.ImageTIC = imageTIC;
WiffPeriod.Sample.WiffFileContent.Add(imageSpectrum);
#if (false)
// TODO -- find out what to do with the 'globalMassMax' value
float anaTime = (float)chrom.GetXValueInSec(nrDataPoints - 1);
chrom.SetToBPC(WiffPeriod.Sample.Index, WiffPeriod.Index, Index, 0, anaTime, minMass, maxMass, 2 * massStepSize);
double tempMass;
chrom.GetYValueRange(out tempMass, out globalMassMax);
chrom.SetToTIC(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
#endif
chrom.WiffFileName = "";
chrom = null;
spec.WiffFileName = "";
spec = null;
}
/// <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;
}
}
private IEnumerable <QuantFile> LoadFiles(IEnumerable <string> filePaths, bool ms3Quant = false)
{
MSDataFile.CacheScans = false;
//int largestQuantPeak = 0;
int i = 0;
foreach (TagInformation tag in UsedTags.Values)
{
tag.UniqueTagNumber = i++;
tag.TotalSignal = 0;
tag.NormalizedTotalSignal = 0;
}
int largestQuantPeak = i - 1;
//int largestQuantPeak = UsedTags.Values.Select(tag => tag.UniqueTagNumber).Concat(new[] {0}).Max();
foreach (string filePath in filePaths)
{
Log("Processing file:\t" + filePath);
OnUpdateLog("Processing File " + filePath + "...");
QuantFile quantFile = new QuantFile(filePath);
StreamReader basestreamReader = new StreamReader(filePath);
int oldProgress = -1;
using (CsvReader reader = new CsvReader(basestreamReader, true))
{
while (reader.ReadNextRecord()) // go through csv and raw file to extract the info we want
{
int scanNumber = int.Parse(reader["Spectrum number"]);
string filenameID = reader["Filename/id"];
string rawFileName = filenameID.Split('.')[0];
bool isDecoy = reader["DEFLINE"].StartsWith("DECOY_");
ThermoRawFile rawFile;
if (!RawFiles.TryGetValue(rawFileName, out rawFile))
{
throw new ArgumentException("Cannot find this raw file: " + rawFileName + ".raw");
}
if (!rawFile.IsOpen)
{
rawFile.Open();
}
int progress = (int)(100 * (double)basestreamReader.BaseStream.Position / basestreamReader.BaseStream.Length);
if (progress != oldProgress)
{
OnProgressUpdate(progress);
oldProgress = progress;
}
//// Set default fragmentation to CAD / HCD
//FragmentationMethod ScanFragMethod = filenameID.Contains(".ETD.")
// ? FragmentationMethod.ETD
// : FragmentationMethod.CAD;
//if (ScanFragMethod == FragmentationMethod.ETD)
//{
// ScanFragMethod = FragmentationMethod.CAD;
// scanNumber += ETDQuantPosition;
//}
// Get the scan object for the sequence ms2 scan
MsnDataScan quantitationMsnScan = rawFile[scanNumber] as MsnDataScan;
double purity = 1;
if (CalculatePurity)
{
double mz = quantitationMsnScan.PrecursorMz;
int charge = quantitationMsnScan.PrecursorCharge;
DoubleRange isolationRange = MzRange.FromDa(mz, PurityWindowInTh);
MSDataScan parentScan = rawFile[quantitationMsnScan.ParentScanNumber];
purity = DeterminePurity(parentScan, mz, charge, isolationRange);
}
if (quantitationMsnScan == null)
{
OnUpdateLog("Spectrum Number " + scanNumber + " is not a valid MS2 scan from: " + rawFile.FilePath + ". Skipping PSM...");
continue;
}
if (MS3Quant)
{
quantitationMsnScan = null;
// Look forward to find associated MS3 quant scan (based on parent scan number)
int ms3ScanNumber = scanNumber + 1;
while (ms3ScanNumber < rawFile.LastSpectrumNumber)
{
if (rawFile.GetParentSpectrumNumber(ms3ScanNumber) == scanNumber)
{
quantitationMsnScan = rawFile[ms3ScanNumber] as MsnDataScan;
break;
}
ms3ScanNumber++;
}
if (quantitationMsnScan == null)
{
OnUpdateLog("Cannot find a MS3 spectrum associated with spectrum number " + scanNumber + ". Skipping PSM...");
continue;
}
}
Tolerance Tolerance = quantitationMsnScan.MzAnalyzer == MZAnalyzerType.IonTrap2D ? ItMassTolerance : FtMassTolerance;
bool isETD = quantitationMsnScan.DissociationType == DissociationType.ETD;
double injectionTime = quantitationMsnScan.InjectionTime;
//var massSpectrum = quantitationMsnScan.MassSpectrum;
var thermoSpectrum = rawFile.GetLabeledSpectrum(quantitationMsnScan.SpectrumNumber);
double noise = 0;
if (NoisebandCap)
{
// Noise is pretty constant over a small region, find the noise of the center of all isobaric tags
MassRange range = new MassRange(UsedTags.Keys[0], UsedTags.Keys[UsedTags.Count - 1]);
if (thermoSpectrum != null)
{
var peak = thermoSpectrum.GetClosestPeak(range.Mean, 500);
if (peak != null)
{
noise = peak.Noise;
}
else
{
OnUpdateLog("Spectrum (#" + quantitationMsnScan.SpectrumNumber + ") has no m/z peaks. Skipping PSM...");
continue;
}
}
else
{
OnUpdateLog("Spectrum (#" + quantitationMsnScan.SpectrumNumber + ") is low-resolution data without noise information. Skipping PSM...");
continue;
}
}
//Dictionary<TagInformation, QuantPeak> peaks = new Dictionary<TagInformation, QuantPeak>();
QuantPeak[] peaks = new QuantPeak[largestQuantPeak + 1];
// Read in the peak data
foreach (TagInformation tag in UsedTags.Values)
{
double tagMz = isETD
? tag.MassEtd
: tag.MassCAD;
var peak = thermoSpectrum.GetClosestPeak(Tolerance.GetRange(tagMz));
QuantPeak qPeak = new QuantPeak(tag, peak, injectionTime, quantitationMsnScan, noise, peak == null && NoisebandCap);
peaks[tag.UniqueTagNumber] = qPeak;
}
PurityCorrect(peaks, isDecoy);
PSM psm = new PSM(filenameID, scanNumber, peaks, purity);
quantFile.AddPSM(psm);
}
}
// Dispose of all raw files
foreach (ThermoRawFile rawFile in RawFiles.Values)
{
rawFile.Dispose();
}
OnUpdateLog("PSMs loaded " + quantFile.Psms.Count);
Log("PSMs Loaded:\t" + quantFile.Psms.Count);
yield return(quantFile);
}
}
/// <summary>
/// Fills this instance data members with the information read from <paramref name="wiffFile"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The data source.</param>
protected override void Initialize(FMANWiffFileClass wiffFile)
{
// set the status information
AppContext.StatusInfo = "Getting wiff-data";
// get the experiment parameters and the experiment object
ITripleQuadMALDI experimentParams = (ITripleQuadMALDI)wiffFile.GetExperimentObject(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
Experiment experiment = (Experiment)wiffFile.GetExperimentObject(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
// get the number of mass MRM transitions
massRanges = experiment.MassRangesCount;
// select 1. MRM trace
FMANChromData anaChrom = new FMANChromData();
anaChrom.WiffFileName = wiffFile.GetWiffFileName();
anaChrom.SetToXICZeroWidth(WiffPeriod.Sample.Index, WiffPeriod.Index, Index, 0);
// dimension the data arrray, the number "data points"
nrDataPoints = anaChrom.GetNumberOfDataPoints();
rawData = new float[massRanges, nrDataPoints];
timeData = new float[nrDataPoints];
dwellTime = new double[massRanges];
massRangeName = new string[massRanges];
massRangeMax = new double[massRanges];
massRangeMin = new double[massRanges];
meanValues = new float[massRanges];
medianValues = new float[massRanges];
// helper for mean and median
double meanSum = 0;
List <float> valuesForMedian = new List <float>();
// loop through the mass ranges
double[] startMass = new double[massRanges];
double[] stopMass = new double[massRanges];
double[] stepMass = new double[massRanges];
for (int actMassRange = 0; actMassRange < massRanges; actMassRange++)
{
// get mass range object
MassRange anaMassRange = (MassRange)experiment.GetMassRange(actMassRange);
startMass[actMassRange] = anaMassRange.QstartMass;
stopMass[actMassRange] = anaMassRange.QstopMass;
stepMass[actMassRange] = anaMassRange.QstepMass;
massRangeName[actMassRange] = Math.Round(startMass[actMassRange], 2).ToString() + " > " + Math.Round(stepMass[actMassRange], 2).ToString();
dwellTime[actMassRange] = anaMassRange.DwellTime;
// select MRM trace
anaChrom.SetToXICZeroWidth(WiffPeriod.Sample.Index, WiffPeriod.Index, Index, (short)actMassRange);
// loop throug the spectrum
massRangeMax[actMassRange] = double.MinValue;
massRangeMin[actMassRange] = double.MaxValue;
meanSum = 0.0;
valuesForMedian.Clear();
for (int actDataPoint = 1; actDataPoint <= nrDataPoints; actDataPoint++)
{
// get the actual value
double anaXValue = anaChrom.GetDataPointXValue(actDataPoint);
double anaYValue = anaChrom.GetDataPointYValue(actDataPoint);
if (anaYValue < massRangeMin[actMassRange])
{
massRangeMin[actMassRange] = anaYValue;
}
if (anaYValue > massRangeMax[actMassRange])
{
massRangeMax[actMassRange] = anaYValue;
}
// now get the actual data
rawData[actMassRange, actDataPoint - 1] = (float)anaYValue;
timeData[actDataPoint - 1] = (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
meanValues[actMassRange] = (float)(meanSum / nrDataPoints);
// calculate the median
valuesForMedian.Sort();
medianValues[actMassRange] = ((valuesForMedian.Count % 2) == 0) ? (float)(valuesForMedian[(valuesForMedian.Count / 2) - 1] + valuesForMedian[valuesForMedian.Count / 2]) / 2.0f : valuesForMedian[valuesForMedian.Count / 2];
}
// get MALDI parmas and assign variables
string strMALDIParams = experimentParams.TripleQuadMALDIParameters;
// x speed in mm/s
xSpeed = float.Parse(strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None)[6]);
//line distance in mm
yDist = float.Parse(strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None)[8]) / 1000;
//time per point in s
xTime = (float)((anaChrom.GetDataPointXValue(nrDataPoints) - anaChrom.GetDataPointXValue(2)) * 60 / (nrDataPoints - 2));
xDist = (float)(int)(xSpeed * xTime * 1000) / 1000;
anaChrom.SetToTIC(WiffPeriod.Sample.Index, WiffPeriod.Index, Index);
// fetch the x1, x2, y1, y2, width and height from the WiffSample instance this experiment belongs to.
double x1 = WiffPeriod.Sample.P1.X;
double y1 = WiffPeriod.Sample.P1.Y;
double x2 = WiffPeriod.Sample.P2.X;
double y2 = WiffPeriod.Sample.P2.Y;
double width = WiffPeriod.Sample.Width;
double height = WiffPeriod.Sample.Height;
//number of poins in x
xPoints = (int)((width) / xSpeed / xTime);
//number of points in y
yPoints = (int)((height) / yDist + 0.5) + 1;
// lineOffset = 1;
// fetch the position data from the WiffSample instance this experiment belongs to.
uint[,] posData = WiffPeriod.Sample.PositionData;
long posDataLength = WiffPeriod.Sample.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;
// ok, we're done...
break;
}
}
long lastNonZeroTimeInPos = -1;
for (long t = posDataLength - 1; t >= 0; t++)
{
if (posData[t, 0] > 0)
{
lastNonZeroTimeInPos = t - 1;
// ok, we're done...
break;
}
}
if (firstNonZeroTimeInPos < 0 || lastNonZeroTimeInPos < 0)
{
// haven't found a valid posData triplet. All time values are zero or less...
// bail out
return;
}
// y2 from the wiff file is not the actual y2 from the stage - replace with value from path file...
y2 = (double)Math.Round((decimal)posData[lastNonZeroTimeInPos, 2] / 1000, 2);
// ...and this has an effect of the ypoints
yPoints = (int)Math.Round((decimal)((y2 - y1) / yDist)) + 1;
#if (false) // experimental method to format the ms-data to the x,y suitable for an image representation
// fet two time stamps from the start and end of chrom file
double tFirstMSDataPoint = anaChrom.GetDataPointXValue(10) * 60 * 1000;
double tLastMSDataPoint = anaChrom.GetDataPointXValue(nrDataPoints - 10) * 60 * 1000;
int positionMarker = 1;
// get the corresponding position from the path file
for (int i = 0; posData[i, 0] < tFirstMSDataPoint; i++)
{
positionMarker = i;
}
double xFirstMSDataPoint =
((tFirstMSDataPoint - posData[positionMarker, 0]) / (posData[positionMarker + 1, 0] - posData[positionMarker, 0])
* (int)(posData[positionMarker + 1, 1] - posData[positionMarker, 1])
+ posData[positionMarker, 1]) / 1000;
double yFirstMSDataPoint = (double)Math.Round((decimal)posData[positionMarker, 2] / 1000, 2);
for (int i = 0; posData[i, 0] < tLastMSDataPoint; i++)
{
positionMarker = i;
}
double xLastMSDataPoint =
((tLastMSDataPoint - posData[positionMarker, 0]) / (posData[positionMarker + 1, 0] - posData[positionMarker, 0])
* (int)(posData[positionMarker + 1, 1] - posData[positionMarker, 1])
+ posData[positionMarker, 1]) / 1000;
double yLastMSDataPoint = (double)Math.Round((decimal)posData[positionMarker, 2] / 1000, 2);
lineOffset = 10 - (xFirstMSDataPoint - x1) / xDist;
if (yPoints % 2 == 0)
{
// even number of scanlines
lineBreak = (((nrDataPoints - 10 - 10)
- (x2 - (float)xFirstMSDataPoint) / xDist
- (yPoints - 2) * (x2 - x1) / xDist
- (x2 - (float)xLastMSDataPoint) / xDist))
/ (yPoints - 1);
}
else
{
// odd number of scanlines
lineBreak = (((nrDataPoints - 10 - 10)
- (x2 - (float)xFirstMSDataPoint) / xDist
- (yPoints - 2) * (x2 - x1) / xDist
- ((float)xLastMSDataPoint - x1) / xDist))
/ (yPoints - 1);
}
//timeOffset = (float)posData[5, 0] / 1000 - (((float)posData[5, 1] / 1000 - x1) / xSpeed);
for (int actMassRange = 0; actMassRange < massRanges; actMassRange++)
{
///////////////////////////////////////////////////////////////////////////////////////////////////////
// format the data into a rectangular, 2 dimensional array of floats that will represent the image data
//
// prepare the data structure
float[][] imageData = new float[xPoints][];
for (int i = 0; i < imageData.Length; i++)
{
imageData[i] = new float[yPoints];
}
// copy the data from wiff file datastream to the rectangular array. Take account of the line offset and
// the line break timings.
for (int y = 0; y < yPoints; y++)
{
int currentPoint;
// currentLine is the offset to the start of the current line in the linear datastream (rawData)
int currentLine = (int)Math.Floor(lineOffset + ((x2 - x1) / xDist + lineBreak) * y);
for (int x = 0; x < xPoints; x++)
{
if (y % 2 == 0)
{
// even y: scan direction: -->
currentPoint = (int)(currentLine + x);
}
else
{
// odd y: scan direction: <--
currentPoint = (int)(currentLine + xPoints - 1 - x);
}
if (currentPoint < nrDataPoints)
{
imageData[x][y] = rawData[actMassRange, currentPoint];
}
else
{
imageData[x][y] = 0;
}
}
}
lineOffset += ((double)dwellTime[actMassRange] + 5) / 1000 * xSpeed / xDist;
#endif
double timeSpanPos = posData[lastNonZeroTimeInPos, 0] / 1000.0 - posData[firstNonZeroTimeInPos, 0] / 1000.0;
double syncTime1 = (float)posData[firstNonZeroTimeInPos, 0] / 1000;
double syncTime2 = (float)posData[lastNonZeroTimeInPos, 0] / 1000;
if (yPoints % 2 == 0)
{
// even number of scanlines
lineBreak = ((syncTime2 - syncTime1)
- (x2 - (float)posData[firstNonZeroTimeInPos, 1] / 1000) / xSpeed
- (yPoints - 2) * (x2 - x1) / xSpeed
- (x2 - (float)posData[lastNonZeroTimeInPos, 1] / 1000) / xSpeed)
/ (yPoints - 1);
//timeOffset = (float)posData[posDataLength - 1, 0] / 1000 + (((float)posData[posDataLength - 1, 1] / 1000 - x1) / xSpeed) - (float)timeData[nrDataPoints - 1] + (float)timeData[0] - 2*xTime; //testing new method
}
else
{
// odd number of scanlines
lineBreak = ((syncTime2 - syncTime1)
- (x2 - (float)posData[firstNonZeroTimeInPos, 1] / 1000) / xSpeed
- (yPoints - 2) * (x2 - x1) / xSpeed
- ((float)posData[lastNonZeroTimeInPos, 1] / 1000 - x1) / xSpeed)
/ (yPoints - 1);
//timeOffset = (float)posData[posDataLength - 1, 0] / 1000 + ((x2 - (float)posData[posDataLength - 1, 1] / 1000) / xSpeed) - (float)timeData[nrDataPoints - 1] + (float)timeData[0] - xTime;//testing new method
}
// MSt lineBreak = lineBreak / xTime;
timeOffset = (float)posData[firstNonZeroTimeInPos, 0] / 1000 - (((float)posData[firstNonZeroTimeInPos, 1] / 1000 - x1) / xSpeed); // original method of calculation
//MSt lineOffset = (timeData[0]-timeOffset) * xSpeed / xDist + .5;
double dwellTimeSum = 0;
// reset the status information
AppContext.StatusInfo = "";
for (int actMassRange = 0; actMassRange < massRanges; actMassRange++)
{
///////////////////////////////////////////////////////////////////////////////////////////////////////
// format the data into a rectangular, 2 dimensional array of floats that will represent the image data
//
// prepare the data structure
float[][] imageData = new float[xPoints][];
for (int i = 0; i < imageData.Length; i++)
{
imageData[i] = new float[yPoints];
}
dwellTimeSum -= (dwellTime[actMassRange] / 1000 / 2);
double optTimeOffset = timeOffset;
double optLineBreak = lineBreak;
if (AppContext.UseApproximation)
{
// Perform the optimization...
HeuristicOptimization(imageData, actMassRange, (x2 - x1), dwellTimeSum, ref optLineBreak, ref optTimeOffset);
}
FormatImageFuzzy(imageData, actMassRange, (x2 - x1), dwellTimeSum, optLineBreak, optTimeOffset);
dwellTimeSum -= (dwellTime[actMassRange] / 1000 / 2);
// create the appropriate dataset and add it to the WiffFileContent object...
string imgName = WiffPeriod.Sample.Name + " : " + massRangeName[actMassRange];
Document doc = WiffPeriod.Sample.WiffFileContent.Document;
//create the meta information data structure and populate with relevant information...
ImageMetaData metaData = new ImageMetaData();
try
{
metaData.Add("Sample Name", typeof(string), WiffPeriod.Sample.Name, false);
metaData.Add("Mass Range", typeof(string), massRangeName[actMassRange], false);
metaData.Add("X1 (mm)", typeof(string), x1.ToString(), false);
metaData.Add("X2 (mm)", typeof(string), x2.ToString(), false);
metaData.Add("Y1 (mm)", typeof(string), y1.ToString(), false);
metaData.Add("Y2 (mm)", typeof(string), y2.ToString(), false);
metaData.Add("Data Points in X", typeof(string), xPoints.ToString(), false);
metaData.Add("Data Points in Y", typeof(string), yPoints.ToString(), false);
metaData.Add("Point Width (mm)", typeof(string), xDist.ToString(), false);
metaData.Add("Point Height (mm)", typeof(string), yDist.ToString(), false);
string[] splitted = strMALDIParams.Split(sepMALDIParams, System.StringSplitOptions.None);
metaData.Add("Laser Frequency (Hz)", typeof(string), splitted[1], false);
metaData.Add("Laser Power (%)", typeof(string), splitted[2], false);
metaData.Add("Ablation Mode", typeof(string), splitted[3], false);
metaData.Add("Skimmer Voltage (V)", typeof(string), splitted[4], false);
metaData.Add("Source Gas", typeof(string), splitted[5], false);
metaData.Add("Raster Speed (mm/s)", typeof(string), splitted[6], false);
metaData.Add("Line Distance (µm)", typeof(string), splitted[8], false);
}
catch (Exception e) { Util.ReportException(e); }
WiffPeriod.Sample.WiffFileContent.Add(new ImageData(doc, imageData, imgName, metaData, (float)massRangeMin[actMassRange], (float)massRangeMax[actMassRange],
(float)meanValues[actMassRange], (float)medianValues[actMassRange], (float)xDist, (float)yDist, (float)startMass[actMassRange], (float)stepMass[actMassRange]));
}
anaChrom.WiffFileName = "";
anaChrom = null;
}
