/// <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;
}
