/// <summary>
/// Gets full heat map data from the <see cref="DataReader"/> that the UIMF is open in.
/// </summary>
/// <param name="uimf">
/// The uimf that data is to be fetched from.
/// </param>
/// <param name="frameNumber">
/// The frame number that data is to be fetched.
/// </param>
/// <returns>
/// The 2d array of doubles with the heat map data.
/// </returns>
private double[,] GetFullHeatmapData(DataReader uimf, int frameNumber)
{
var global = uimf.GetGlobalParams();
var endScan = uimf.GetFrameParams(frameNumber).Scans;
var endBin = global.Bins;
return(uimf.AccumulateFrameData(frameNumber, frameNumber, false, 1, endScan, 1, endBin, 1, 1));
}
public void ReadAllFramesAndScans()
{
if (!File.Exists(mTestUIMFFilePath))
{
reportProgress("UIMFFile not found. Input file path was: " + mTestUIMFFilePath);
return;
}
var datareader = new DataReader(mTestUIMFFilePath);
//--------------------------------------------------------------------------Get Global parameters
var gp = datareader.GetGlobalParams();
reportProgress();
reportProgress();
reportProgress("Displaying some global parameters...");
#pragma warning disable 618
var legacyGlobalParams = datareader.GetGlobalParameters();
#pragma warning restore 618
reportProgress("DateStarted_Legacy= " + legacyGlobalParams.DateStarted);
reportProgress("DateStarted= " + gp.GetValue(GlobalParamKeyType.DateStarted));
reportProgress("NumBins= " + gp.Bins);
reportProgress("NumFrames= " + gp.NumFrames);
reportProgress("Pre-caching all frame parameters...");
datareader.PreCacheAllFrameParams();
int frameCountWithError = 0;
for (var frameNum = 1; frameNum <= gp.NumFrames; frameNum++)
{
var fp = datareader.GetFrameParams(frameNum);
if (fp == null)
{
continue;
}
if (fp.CalibrationSlope <= 0.0001)
{
Console.WriteLine("Frame " + frameNum + ", Slope is 0 (or negative)");
}
if (Math.Abs(fp.CalibrationIntercept) < Single.Epsilon)
{
Console.WriteLine("Frame " + frameNum + ", Intercept is 0");
}
var startScan = 0;
var endScan = fp.GetValueInt32(FrameParamKeyType.Scans);
var startBin = 1;
var endBin = gp.Bins;
var valuesPerPixelX = 100;
var valuesPerPixelY = 100;
// Note that AccumulateFrameData is used by the UimfViewer and by Atreyu
var frameData = datareader.AccumulateFrameData(frameNum, frameNum, false, startScan, endScan, startBin, endBin, valuesPerPixelX, valuesPerPixelY);
var topIndex1 = frameData.GetUpperBound(0);
var topIndex2 = frameData.GetUpperBound(1);
var nonZeroCount = 0;
for (var i = 0; i <= topIndex1; i++)
{
for (var j = 0; j <= topIndex2; j++)
{
if (frameData[i, j] > 0)
{
// Console.Write(frameData[i, j] + " ");
nonZeroCount++;
}
}
}
if (frameNum % 25 == 0)
{
Console.WriteLine();
Console.WriteLine("Frame " + frameNum + " has " + nonZeroCount + " non-zero points");
}
if (nonZeroCount == 0)
{
Console.WriteLine(" - Error, all points have an intensity of zero; this should not happen");
frameCountWithError++;
}
var frameScanInfo = datareader.GetFrameScans(frameNum);
if (frameNum % 25 == 0)
{
foreach (var scanInfo in frameScanInfo)
{
if (scanInfo.Scan % 100 == 0)
{
Console.WriteLine(" Scan " + scanInfo.Scan.ToString().PadLeft(3) + " has BPI = " +
scanInfo.BPI + " at " +
scanInfo.BPI_MZ.ToString("0.0") + " m/z, TIC = " + scanInfo.TIC +
" and drift time " + scanInfo.DriftTime.ToString("0.0") + " msec");
}
}
}
}
Console.WriteLine();
Console.WriteLine("Loaded data from " + gp.NumFrames + " frames; count with error: " + frameCountWithError);
}
private void WriteRun(XmlWriter writer, string outputPath, DataReader reader, VoltageGroup voltageGroup)
{
writer.WriteStartElement("run");
string dataset = Path.GetFileNameWithoutExtension(outputPath);
writer.WriteAttributeString("id", dataset);
writer.WriteAttributeString("defaultInstrumentConfigurationRef", "IC");
writer.WriteAttributeString("startTimeStamp", this.dateTime);
writer.WriteStartElement("spectrumList");
writer.WriteAttributeString("count", this.scans.ToString(CultureInfo.InvariantCulture));
int startingFrame = voltageGroup.FirstFrameNumber;
int endingFrame = voltageGroup.LastFrameNumber;
Console.Write("Summing frame[{0} - {1}]... ", startingFrame, endingFrame);
double[,] summedIntensities = reader.AccumulateFrameData(startingFrame, endingFrame, false, 1, this.scans, 1, this.bins, -1, -1);
// Use dirft time scan as LC scan to massage skyline
for (int lcScan = 1; lcScan <= this.scans; lcScan++)
{
float[] mzArray;
float[] intensityArray;
this.GetMzIntensityArrayAtScan(summedIntensities, lcScan, out mzArray, out intensityArray);
double mzLow = mzArray[0];
double mzHigh = mzArray[mzArray.Count()-1];
// Write the bins as mass spectrum
writer.WriteStartElement("spectrum");
writer.WriteAttributeString("index", String.Format("{0}", lcScan - 1));
writer.WriteAttributeString("id", String.Format("frame={0} scan={1} frameType={2}", 1, lcScan, 1));
writer.WriteAttributeString("defaultArrayLength", mzArray.Count().ToString(CultureInfo.InvariantCulture));
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000511");
writer.WriteAttributeString("name", "ms level");
writer.WriteAttributeString("value", "1");
writer.WriteEndElement();
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000579");
writer.WriteAttributeString("name", "MS1 spectrum");
writer.WriteAttributeString("value", "");
writer.WriteEndElement();
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000128");
writer.WriteAttributeString("name", "profile spectrum");
writer.WriteAttributeString("value", "");
writer.WriteEndElement();
writer.WriteStartElement("scanList");
writer.WriteAttributeString("count", "1");
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000795");
writer.WriteAttributeString("name", "no combination");
writer.WriteAttributeString("value", "");
writer.WriteEndElement();
writer.WriteStartElement("scan");
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000016");
writer.WriteAttributeString("name", "scan start time");
writer.WriteAttributeString("value", reader.GetDriftTime(voltageGroup.FirstFrameNumber, lcScan, true).ToString(CultureInfo.InvariantCulture));
writer.WriteAttributeString("unitCvRef", "UO");
writer.WriteAttributeString("unitAccession", "UO:0000031");
writer.WriteAttributeString("unitName", "minute");
writer.WriteEndElement();
writer.WriteStartElement("scanWindowList");
writer.WriteAttributeString("count", "1");
writer.WriteStartElement("scanWindow");
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000501");
writer.WriteAttributeString("name", "scan window lower limit");
writer.WriteAttributeString("value", mzLow.ToString(CultureInfo.InvariantCulture));
writer.WriteAttributeString("unitCvRef", "MS");
writer.WriteAttributeString("unitAccession", "MS:1000040");
writer.WriteAttributeString("unitName", "m/z");
writer.WriteEndElement();
writer.WriteStartElement("cvParam");
writer.WriteAttributeString("cvRef", "MS");
writer.WriteAttributeString("accession", "MS:1000500");
writer.WriteAttributeString("name", "scan window upper limit");
writer.WriteAttributeString("value", mzHigh.ToString(CultureInfo.InvariantCulture));
writer.WriteAttributeString("unitCvRef", "MS");
writer.WriteAttributeString("unitAccession", "MS:1000040");
writer.WriteAttributeString("unitName", "m/z");
writer.WriteEndElement();
// scan window
writer.WriteEndElement();
// scan window list
writer.WriteEndElement();
// scan
writer.WriteEndElement();
// scan list
writer.WriteEndElement();
this.WriteBinaryDataArrays(mzArray, intensityArray, writer);
// spectrum
writer.WriteEndElement();
}
// spectrum list
writer.WriteEndElement();
// run
writer.WriteEndElement();
}
