private void ReadFrameMsMidacSpecData(MidacSpecFormat specFormat, ref Stopwatch sw, int[] frameNumbers, int numDriftBins)
{
sw.Start();
int minDBin = 0;
int maxDBin = numDriftBins - 1;
for (int i = 0; i < frameNumbers.Length; i++)
{
int frame = frameNumbers[i];
for (int dbin = minDBin; dbin <= maxDBin; dbin++)
{
IMidacSpecDataMs specData = m_reader.FrameMs(frame, dbin, specFormat, true) as IMidacSpecDataMs;
// To access the CE range:
// IDoubleRange ceRange = specData.FragmentationEnergyRange;
AnalyzeSpectrum(specData);
}
}
sw.Stop();
}
private void ReadFrameMsReuseMidacSpecData(MidacSpecFormat specFormat, ref Stopwatch sw, int[] frameNumbers, int driftBins)
{
sw.Start();
int minDBin = 0;
int maxDBin = driftBins - 1;
IMidacSpecDataMs specData = null;
for (int i = 0; i < frameNumbers.Length; i++)
{
int frame = frameNumbers[i];
for (int dbin = minDBin; dbin <= maxDBin; dbin++)
{
m_reader.FrameMs(frame, dbin, specFormat, true, ref specData);
AnalyzeSpectrum(specData);
}
}
sw.Stop();
}
private void ReadProfTfsMidacSpecDataExternal(MidacSpecFormat specFmt, ref Stopwatch sw, int[] frameNumbers)
{
sw.Start();
int lastLength = -1;
IIntRange[] xIdxRanges = null;
bool doSum = chkTfsDoSumming.Checked;
int nFrames = 0;
int nDummy = 0;
List <IDoubleRange> mzRanges = new List <IDoubleRange>();
for (int i = 0; i < frameNumbers.Length; i++)
{
int frame = frameNumbers[i];
double tic = 0;
// get the TFS
IMidacSpecDataMs specData = m_reader.ProfileTotalFrameMs(specFmt, frame);
++nFrames;
if (specFmt == MidacSpecFormat.Metadata)
{
if (specData != null)
{
if (specData.NonZeroPoints > 0)
{
++m_msCount;
m_sumNzPoints += specData.NonZeroPoints;
// For testing, we don't want the maximum array size, we want the number of points
// actually returned -- which is zero for Metadata only calls.
// m_sumPoints += specData.MaxProfilePoints;
}
}
}
else
{
if (frame == 1 || frame == 17 || frame == 18 || frame == 96 || frame == 97 || frame == 122)
{
nDummy = frame;
}
// Sum abundances over specified range(s)
if (specData != null && specData.XArray != null && specData.XArray.Length > 0)
{
++m_msCount;
m_sumNzPoints += specData.NonZeroPoints;
// Again, actually returned points, not maximum number for zero-filled spectra
m_sumPoints += specData.XArray.Length;
if (doSum)
{
if (specFmt == MidacSpecFormat.Profile)
{
// We can pre-calculate array index values corresponding to the m/z
// inclusion limits.
if (lastLength != specData.XArray.Length)
{
// convert ranges to x- and y-array index equivalent
xIdxRanges = GetXIndexRanges(specData.XArray[0], specData.XArray.Length, m_ftBinRanges);
lastLength = specData.XArray.Length;
}
// sum all ion abundances falling in each m/z range
foreach (IIntRange xIdxRange in xIdxRanges)
{
for (int j = xIdxRange.Min; j <= xIdxRange.Max; j++)
{
tic += specData.YArray[j];
}
}
}
else
{
// With sparse arrays, we cannot.
double[] xArray = specData.XArray;
float[] yArray = specData.YArray;
int nextIdx = 0;
int maxIdx = xArray.Length - 1;
// ToDo: if there are multiple m/z ranges, sort them in increasing m/z and
// coalesce any that overlap
foreach (IDoubleRange mzRange in m_mzRanges)
{
double min = mzRange.Min;
double max = mzRange.Max;
do
{
double mz = xArray[nextIdx];
if (mz < min)
{
++nextIdx;
}
else if (mz > max)
{
break;
}
else
{
tic += yArray[nextIdx++];
}
} while (nextIdx <= maxIdx);
}
}
}
}
m_tic += tic;
}
}
sw.Stop();
}
