/// <summary>
/// Writes the imaging data specified by the given <see cref="ImageSpectrumData"/> object
/// to a file specified by the file name.
/// </summary>
/// <param name="specData"><see cref="ImageSpectrumData"/> object to be written.</param>
/// <param name="fileName">The file to which the image data will be written.</param>
/// <returns>A <see cref="bool"/> value indicating the success of the write operation.</returns>
private bool Write(ImageSpectrumData specData, string fileName)
{
if (specData == null)
{
throw new ArgumentNullException("specData");
}
if (string.IsNullOrEmpty(fileName))
{
throw new ArgumentException("fileName");
}
// setup the three stream of an Analyze file...
var imgStream = new FileStream(fileName, FileMode.OpenOrCreate, FileAccess.Write);
var hdrStream = new FileStream(fileName.Replace(".img", ".hdr"), FileMode.Create, FileAccess.Write);
var ttmStream = new FileStream(fileName.Replace(".img", ".t2m"), FileMode.Create, FileAccess.Write);
// and assign to writers...
var imgWriter = new BinaryWriter(imgStream);
var hdrWriter = new BinaryWriter(hdrStream);
var ttmWriter = new BinaryWriter(ttmStream);
// write the header file.
// this is dark, obscure and intrinsic...
// ToDo JP 08/02/12 replace the stuff below with AnalyseFileHeaderObject
hdrWriter.BaseStream.Position = 0;
hdrWriter.Write(384);
hdrWriter.BaseStream.Position = 4;
hdrWriter.Write(" 16");
hdrWriter.BaseStream.Position = 32;
hdrWriter.Write((short)16384);
hdrWriter.BaseStream.Position = 38;
hdrWriter.Write((byte)114);
hdrWriter.BaseStream.Position = 40;
hdrWriter.Write((short)4);
hdrWriter.BaseStream.Position = 42;
hdrWriter.Write((short)specData.DataSets.Count); // There will be files that contain parameter greater than 16 bit
hdrWriter.BaseStream.Position = 44;
hdrWriter.Write((short)specData.XPoints);
hdrWriter.BaseStream.Position = 46;
hdrWriter.Write((short)specData.YPoints);
hdrWriter.BaseStream.Position = 48;
hdrWriter.Write((short)1);
hdrWriter.BaseStream.Position = 70; // this read the data type
hdrWriter.Write((short)16);
hdrWriter.BaseStream.Position = 72;
hdrWriter.Write((short)16);
hdrWriter.BaseStream.Position = 76; // step size x
hdrWriter.Write((float)1);
hdrWriter.BaseStream.Position = 80;
hdrWriter.Write(specData.Dx);
hdrWriter.BaseStream.Position = 84;
hdrWriter.Write(specData.Dy);
hdrWriter.BaseStream.Position = 88;
hdrWriter.Write((float)1);
foreach (MetaDataItem mdi in specData.MetaData)
{
switch (mdi.Name)
{
case "X1 (mm)":
hdrWriter.BaseStream.Position = 253;
hdrWriter.Write((ushort)float.Parse(mdi.ValueString));
break;
case "Y1 (mm)":
hdrWriter.BaseStream.Position = 255;
hdrWriter.Write((ushort)float.Parse(mdi.ValueString));
break;
}
}
// and cleanup
hdrWriter.BaseStream.Position = 383;
hdrWriter.Write((byte)0);
hdrWriter.Close();
// write the image formatted MS data...
for (int y = 0; y < specData.YPoints; y++)
{
for (int x = 0; x < specData.XPoints; x++)
{
foreach (ImageData imgData in specData.DataSets)
{
float intensity = imgData.Data[x][y];
imgWriter.Write(intensity);
}
}
}
// and cleanup
imgWriter.Close();
// write calibration file
for (int i = 0; i < specData.DataSets.Count; i++)
{
// TODO JP - should this contain the contents of specData.MassCal?
// specData.MassStep is now 1 [specData.MinMass + (specData.MassStep * i)]
ttmWriter.Write(specData.MassCal[0] + i); //specData.MinMass
}
// and cleanup
ttmWriter.Close();
return(true);
}
/// <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;
}
}
