private void ReadTic(ref Stopwatch sw, int[] frameNumbers)
{
IMidacMsFiltersChrom chromFilters = MidacFileAccess.DefaultMsChromFilters;
if (rbAllIonsHigh.Enabled)
{
if (rbAllIonsHigh.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.HighEnergy;
}
else if (rbAllIonsLow.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.LowEnergy;
}
}
sw.Start();
IMidacChromDataMs chromData = m_reader.Chromatogram(ChromatogramType.TotalIon, false, chromFilters);
float[] yArray = chromData.YArray;
if (yArray != null)
{
for (int i = 0; i < yArray.Length; i++)
{
m_tic += yArray[i];
}
}
sw.Stop();
}
private void cbOpen_Click(object sender, EventArgs e)
{
if (string.IsNullOrEmpty(txtFilePath.Text))
{
MessageBox.Show("No input file is specified");
return;
}
string filePath = txtFilePath.Text.Trim();
if (!Directory.Exists(filePath))
{
MessageBox.Show(string.Format("Folder {0} does not exist.", filePath));
return;
}
if (!MidacFileAccess.FileHasImsData(filePath))
{
lbFileContents.Text = "File does not have IM-MS data (not opened)";
lbFileContents2.Text = "";
gbCCS.Enabled = false;
return;
}
if (m_reader != null)
{
m_reader.Close();
}
m_reader = null;
// Returns a reader alredy opened to the specified file path
m_reader = MidacFileAccess.ImsDataReader(filePath);
m_currentFilePath = filePath;
// Get overall file metadata
IMidacFileInfo fileInfo = m_reader.FileInfo;
// show something about the contents of the file
string tfsType = "";
if (m_reader.HasPeakTfsSpectra)
{
tfsType += "Peak";
}
if (m_reader.HasProfileTfsSpectra)
{
tfsType += tfsType.Length > 0 ? " and Profile" : "Profile";
}
lbFileContents.Text = string.Format("{0} frames with max of {1} drift bins/frame; with {2} Total Frame Spectra for each frame",
fileInfo.NumFrames,
fileInfo.MaxNonTfsMsPerFrame,
tfsType);
gbCCS.Enabled = m_reader.HasSingleFieldCcsInformation;
lbFileContents2.Text = string.Format("{0} prepared for CCS conversions", m_reader.HasSingleFieldCcsInformation ? "Is" : "Is NOT");
// If there are high/low fragmentation frames, find out how many
if (fileInfo.HasHiLoFragData)
{
IMidacMsFiltersChrom chromFilters = MidacFileAccess.DefaultMsChromFilters;
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.HighEnergy;
int numHighFrames = m_reader.FilteredFrameNumbers(chromFilters).Length;
chromFilters.FragmentationClass = FragmentationClass.LowEnergy;
int numLowFrames = m_reader.FilteredFrameNumbers(chromFilters).Length;
rbAllIonsAll.Enabled = true;
rbAllIonsHigh.Enabled = true;
rbAllIonsLow.Enabled = true;
lbStatusAllIons.Visible = true;
lbStatusAllIons.Text = string.Format("{0} High-CE frames; {1} Low-CE frames", numHighFrames, numLowFrames);
}
else
{
rbAllIonsAll.Enabled = false;
rbAllIonsHigh.Enabled = false;
rbAllIonsLow.Enabled = false;
lbStatusAllIons.Visible = false;
}
// Force read of some data before we start; gets some assertions out of the way.
IMidacUnitConverter converter = m_reader.FrameInfo(1).FrameUnitConverter;
}
private void cbReadFrameMs_Click(object sender, EventArgs e)
{
if (m_reader == null)
{
MessageBox.Show("File is not open");
return;
}
int reps = 1;
int.TryParse(txtReps.Text, out reps);
try
{
int[] frameNumbers = null;
if (rbAllIonsHigh.Enabled)
{
IMidacMsFiltersChrom chromFilters = MidacFileAccess.DefaultMsChromFilters;
if (rbAllIonsHigh.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.HighEnergy;
}
else if (rbAllIonsLow.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.LowEnergy;
}
frameNumbers = m_reader.FilteredFrameNumbers(chromFilters);
}
else
{
frameNumbers = new int[m_reader.FileInfo.NumFrames];
for (int i = 0; i < frameNumbers.Length; i++)
{
frameNumbers[i] = i + 1;
}
}
cbBrowse.Enabled = false;
cbOpen.Enabled = false;
cbReadProfileTfs.Enabled = false;
cbReadFrameMs.Enabled = false;
gbProfileTfsFmt.Enabled = false;
// int numFrames = m_reader.FileInfo.NumFrames;
int numDriftBins = m_reader.FileInfo.MaxNonTfsMsPerFrame;
Stopwatch sw = new Stopwatch();
sw.Reset();
lbStatus.Text = "Processing";
this.Refresh();
m_msCount = 0;
m_tic = 0.0;
m_sumPoints = 0;
m_sumNzPoints = 0;
((MidacImsFileReader)m_reader).ClearCounts();
for (int i = reps; i > 0; i--)
{
if (rbFrameMsMidacSpecData.Checked)
{
ReadFrameMsMidacSpecData(MidacSpecFormat.Profile, ref sw, frameNumbers, numDriftBins);
}
if (rbFrameZtMsMidacSpecData.Checked)
{
ReadFrameMsMidacSpecData(MidacSpecFormat.ZeroTrimmed, ref sw, frameNumbers, numDriftBins);
}
if (rbFrameZbMsMidacSpecData.Checked)
{
ReadFrameMsMidacSpecData(MidacSpecFormat.ZeroBounded, ref sw, frameNumbers, numDriftBins);
}
if (rbFrameMdMsMidacSpecData.Checked)
{
ReadFrameMsMidacSpecData(MidacSpecFormat.Metadata, ref sw, frameNumbers, numDriftBins);
}
if (rbFrameMsReuseMidacSpecData.Checked)
{
ReadFrameMsReuseMidacSpecData(MidacSpecFormat.Profile, ref sw, frameNumbers, numDriftBins);
}
#if PNNL_VERSION
// placeholder for internal tests
if (rbFrameMsArrayOfIters.Checked)
{
ReadFrameMsArrayOfIters(ref sw, numFrames, numDriftBins);
}
#endif
}
((MidacImsFileReader)m_reader).CheckCounts();
m_msCount /= reps;
double ticks = sw.ElapsedTicks;
double ticksPerSec = Stopwatch.Frequency;
double milliseconds = (1000.0 * ticks) / ticksPerSec / reps;
m_tic /= reps;
m_sumPoints /= reps;
m_sumNzPoints /= reps;
IMidacFileInfo info = m_reader.FileInfo;
if (chkFrameMsDoSumming.Checked && !rbFrameMdMsMidacSpecData.Checked)
{
lbStatus.Text =
string.Format("Done in {0:##,#.###} ms ({1:##,#.###} us/spectrum; {2:##,#} non-empty spectra; TIC = {3:##,#}; points = {4:##,#}; NZ = {5:##,#})",
milliseconds,
1000 * milliseconds / m_msCount,
m_msCount,
m_tic,
m_sumPoints,
m_sumNzPoints);
}
else
{
// no TIC
lbStatus.Text =
string.Format("Done in {0:##,#.###} ms ({1:##,#.###} us/spectrum; {2:##,#} non-empty spectra; points = {3:##,#}; NZ = {4:##,#})",
milliseconds,
1000 * milliseconds / m_msCount,
m_msCount,
m_sumPoints,
m_sumNzPoints);
}
}
finally
{
cbBrowse.Enabled = true;
cbOpen.Enabled = true;
cbReadProfileTfs.Enabled = true;
cbReadFrameMs.Enabled = true;
gbProfileTfsFmt.Enabled = true;
}
}
private void cbReadProfileTfs_Click(object sender, EventArgs e)
{
if (m_reader == null)
{
MessageBox.Show("File is not open");
return;
}
if (!m_reader.HasProfileTfsSpectra)
{
MessageBox.Show("This files doesn't have profile Total Frame Sepctra");
return;
}
int reps = 1;
int.TryParse(txtReps.Text, out reps);
// Get m/z ranges
m_doTic = rbChroTic.Checked;
m_mzRanges = new List <IDoubleRange>();
if (m_doTic)
{
double maxMz = m_reader.FileInfo.MaxFlightTimeBin;
m_reader.FileUnitConverter.Convert(MidacUnits.FlightTimeBinIndex, MidacUnits.MassToCharge, ref maxMz);
m_mzRanges.Add(new DoubleRange(5.0, maxMz, MidacUnits.MassToCharge));
}
else
{
IDoubleRange dr = GetMzRange(txtEic1.Text);
if (!DoubleRange.IsNullOrEmpty(dr))
{
m_mzRanges.Add(dr);
}
dr = GetMzRange(txtEic2.Text);
if (!DoubleRange.IsNullOrEmpty(dr))
{
m_mzRanges.Add(dr);
}
dr = GetMzRange(txtEic3.Text);
if (!DoubleRange.IsNullOrEmpty(dr))
{
m_mzRanges.Add(dr);
}
dr = GetMzRange(txtEic4.Text);
if (!DoubleRange.IsNullOrEmpty(dr))
{
m_mzRanges.Add(dr);
}
dr = GetMzRange(txtEic5.Text);
if (!DoubleRange.IsNullOrEmpty(dr))
{
m_mzRanges.Add(dr);
}
}
m_ftBinRanges = new List <IIntRange>();
IMidacUnitConverter converter = m_reader.FileUnitConverter;
foreach (IDoubleRange mzRange in m_mzRanges)
{
IDoubleRange mzClone = mzRange.Clone();
converter.Convert(MidacUnits.FlightTimeBinIndex, ref mzClone);
m_ftBinRanges.Add(new IntRange((int)mzClone.Min, (int)mzClone.Max));
}
try
{
cbBrowse.Enabled = false;
cbOpen.Enabled = false;
cbReadProfileTfs.Enabled = false;
cbReadFrameMs.Enabled = false;
gbProfileTfsFmt.Enabled = false;
int[] frameNumbers = null;
if (rbAllIonsHigh.Enabled)
{
IMidacMsFiltersChrom chromFilters = MidacFileAccess.DefaultMsChromFilters;
if (rbAllIonsHigh.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.HighEnergy;
}
else if (rbAllIonsLow.Checked)
{
chromFilters.ApplicableFilters = ApplicableFilters.FragmentationClass;
chromFilters.FragmentationClass = FragmentationClass.LowEnergy;
}
frameNumbers = m_reader.FilteredFrameNumbers(chromFilters);
}
else
{
frameNumbers = new int[m_reader.FileInfo.NumFrames];
for (int i = 0; i < frameNumbers.Length; i++)
{
frameNumbers[i] = i + 1;
}
}
Stopwatch sw = new Stopwatch();
sw.Reset();
lbStatus.Text = "Processing";
this.Refresh();
m_msCount = 0;
m_tic = 0.0;
m_sumPoints = 0;
m_sumNzPoints = 0;
for (int i = reps; i > 0; i--)
{
if (rbProfTfsFrameInfo.Checked)
{
ReadFrameInfo(ref sw, frameNumbers);
}
#if ENABLE_MHDAC_TESTS
if (rbProfTfsMhdac.Checked)
{
ReadProfTfsMhdac(ref sw, frameNumbers);
}
#endif
if (rbProfTfsMidacSpecDataExternal.Checked)
{
ReadProfTfsMidacSpecDataExternal(MidacSpecFormat.Profile, ref sw, frameNumbers);
}
if (rbProfZtTfsMidacSpecDataExternal.Checked)
{
ReadProfTfsMidacSpecDataExternal(MidacSpecFormat.ZeroTrimmed, ref sw, frameNumbers);
}
if (rbProfZbTfsMidacSpecDataExternal.Checked)
{
ReadProfTfsMidacSpecDataExternal(MidacSpecFormat.ZeroBounded, ref sw, frameNumbers);
}
if (rbProfMdTfsMidacSpecDataExternal.Checked)
{
ReadProfTfsMidacSpecDataExternal(MidacSpecFormat.Metadata, ref sw, frameNumbers);
}
if (rbReadTic.Checked)
{
ReadTic(ref sw, frameNumbers);
}
#if INTERNAL_TEST
// placeholder for internal tests
#endif
}
double ticks = sw.ElapsedTicks;
double ticksPerSec = Stopwatch.Frequency;
double milliseconds = 1000.0 * ticks / ticksPerSec / reps;
m_tic /= reps;
m_sumPoints /= reps;
m_sumNzPoints /= reps;
m_msCount /= reps;
if (rbProfTfsFrameInfo.Checked)
{
lbStatus.Text = string.Format("Done in {0:F3} ms ({1:F3} us/frame; {2} non-empty frames)",
milliseconds,
1000 * milliseconds / m_msCount,
m_msCount);
}
else if (rbReadTic.Checked)
{
lbStatus.Text = string.Format("Done in {0:F3} ms; (TIC = {1})",
milliseconds,
m_tic);
}
else
{
if (chkTfsDoSumming.Checked && !rbProfMdTfsMidacSpecDataExternal.Checked)
{
lbStatus.Text =
string.Format("Done in {0:##,0.###} ms ({1:##,0.###} us/frame; {2:##,0} non-empty spectra; TIC = {3:##,#}; Points = {4:##,0}; NZ = {5:##,0})",
milliseconds,
1000 * milliseconds / m_msCount,
m_msCount,
m_tic,
m_sumPoints,
m_sumNzPoints);
}
else
{
// no TIC value
lbStatus.Text =
string.Format("Done in {0:##,0.###} ms ({1:##,0.###} us/frame; {2:##,0} non-empty spectra; Points = {3:##,0}; NZ = {4:##,0})",
milliseconds,
1000 * milliseconds / m_msCount,
m_msCount,
m_sumPoints,
m_sumNzPoints);
}
}
}
finally
{
cbBrowse.Enabled = true;
cbOpen.Enabled = true;
cbReadProfileTfs.Enabled = true;
cbReadFrameMs.Enabled = true;
gbProfileTfsFmt.Enabled = true;
}
}
