private void ScanArriveHandler(object sender, MsScanEventArgs e)
{
IMsScan scan = e.GetScan();
if (scan == null)
{
WriteLog("Empty scan");
}
else
{
string accessId = null;
scan.Trailer.TryGetValue("Access id:", out accessId);
WriteLog(string.Format("Received a new scan (scan number={0}, runningNumber={1}) containing {2} peaks",
scan.Header["Scan"], accessId, scan.CentroidCount));
// dump header
foreach (KeyValuePair <string, string> kvp in scan.Header)
{
string msg = string.Format("- Header\tKey = {0}, Value = {1}", kvp.Key, kvp.Value);
WriteLog(msg);
}
}
// run user scan event handler
scanHandler(scan);
}
void OnMsScanArrived(object sender, MsScanEventArgs e)
{
var lastScan1 = ias.InstMSScanContainer.GetLastMsScan();
var currentScan = e.GetScan();
UpdateScanNumber(currentScan);
var header = currentScan.Header;
int msOrder = int.Parse(header["MSOrder"]);
if (msOrder < 2)
{
return;
}
if (header.ContainsKey("PrecursorMass[0]"))
{
var precursorMass = decimal.Parse(currentScan.Header["PrecursorMass[0]"]);
if (DBHelper.precursors.ContainsKey((int)precursorMass))
{
//put the top 100 in the second table.
DBHelper.StoreScan(currentScan, maxTargets);
}
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
// If examining code takes longer, in particular for some scans, it is wise
// to use a processing queue in order to get the system as responsive as possible.
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("==================================================");
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
//TO THINK: If the coming scan is MS2 scan, start the timing of the scan precursor into exclusion list. Currently, start when add the scan precursor.
if (!IsTakeOverScan(scan))
{
if (IsMS1Scan(scan))
{
Console.WriteLine("MS1 Scan arrived.");
if (!TimeIsOver)
{
AddScanIntoQueueAction(scan);
}
}
else
{
Console.WriteLine("MS2 Scan arrived.");
}
}
else if (!firstFullScanPlaced)
{
FullScan.PlaceFullScan(m_scans, Parameters);
Console.WriteLine("Place First User defined Full Scan.");
firstFullScanPlaced = true;
}
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
string accessId;
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
// The access ID gives a feedback about placed scans or scans generated by the instrument.
scan.SpecificInformation.TryGetValue("Access Id:", out accessId);
Console.WriteLine("{0:HH:mm:ss,fff} scan {1} arrived", DateTime.Now, accessId);
////// The common part is shared by all Thermo Fisher instruments, these settings mainly form the so called filter string
////// which also appears on top of each spectrum in many visualizers.
//Console.WriteLine("----------------Common--------------");
//Dump("Common", scan.CommonInformation);
////// The specific part is individual for each instrument type. Many values are shared by different Exactive Series models.
//Console.WriteLine("----------------Specific--------------");
// Dump("Specific", scan.SpecificInformation);
//Dump(scan);
var ib = IsBoxCarScan(scan);
Console.WriteLine("IsBoxCar Scan: {0}", ib);
FullScan.PlaceFullScan(m_scans, Parameters);
//List<double> dynamicBoxCarRange = new List<double> { 600, 700, 800, 900, 1000 };
//BoxCarScan.PlaceBoxCarScan(m_scans, Parameters, dynamicBoxCarRange);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, 750);
BoxCarScan.PlaceStaticBoxCarScan(m_scans, Parameters);
}
}
private void Orbitrap_MsScanArrived_TakeOver(object sender, MsScanEventArgs e)
{
using (IMsScan scan = (IMsScan)e.GetScan())
{
TakeOverInstrumentMessage(scan);
}
}
//The IMsScan will arrive at this method
//It will be sent to DataProcessor to be parsed into a Scan object, and the IMsScan will be disposed to prevent blocking shared memory
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
log.Debug("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
DataProcessor.ParseIMsScan(scan);
}
}
/// <summary>
/// When a new scan arrives we dump that information in verbose mode.
/// </summary>
/// <param name="sender">doesn't matter</param>
/// <param name="e">used to access the scan information</param>
private void ScanContainer_ScanArrived(object sender, MsScanEventArgs e)
{
if (!Arguments.Verbose)
{
Console.WriteLine("Scan arrived");
// As an example we access all centroids
using (IMsScan scan = (/* V2 */ IMsScan)e.GetScan())
{
m_integral += AllProfInts(scan);
}
return;
}
// Dump the scan content.
using (IMsScan scan = (/* V2 */ IMsScan)e.GetScan())
{
DumpScan("Scan arrived", scan);
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
// If examining code takes longer, in particular for some scans, it is wise
// to use a processing queue in order to get the system as responsive as possible.
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
// If examining code takes longer, in particular for some scans, it is wise
// to use a processing queue in order to get the system as responsive as possible.
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
Console.WriteLine("Noise: " + string.Join("; ", scan.NoiseBand.Take(5).Select(n => string.Format("{0:F2},{1:0.0e0}", n.Mz, n.Intensity))));
Console.WriteLine("Centroids: " + string.Join("; ", scan.Centroids.Take(5).Select(n => string.Format("{0:F2},{1:0.0e0},z={2},R={3}", n.Mz, n.Intensity, n.Charge, n.Resolution))));
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
string accessId;
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
// The access ID gives a feedback about placed scans or scans generated by the instrument.
scan.SpecificInformation.TryGetValue("Access Id:", out accessId);
Console.WriteLine("{0:HH:mm:ss,fff} scan {1} arrived", DateTime.Now, accessId);
PlaceScan();
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
// The common part is shared by all Thermo Fisher instruments, these settings mainly form the so called filter string
// which also appears on top of each spectrum in many visualizers.
Dump("Common", scan.CommonInformation);
// The specific part is individual for each instrument type. Many values are shared by different Exactive Series models.
Dump("Specific", scan.SpecificInformation);
}
}
void scanArrived_Response(object sender, MsScanEventArgs e)
{
try
{
Console.WriteLine("Scan arrived.");
logfile.WriteLine("Scan arrived.");
if (!authorized_for_run)
{
Console.WriteLine("Ignoring pre-emptive scan.");
logfile.WriteLine("Ignoring pre-emptive scan.");
return;
}
else if (!accepting_scans)
{
Console.WriteLine("Ignoring wait-time scan.");
logfile.WriteLine("Ignoring wait-time scan.");
return;
}
IMsScan scandata = e.GetScan();
if (runTimeKeeper.Elapsed > intendedRunTime)
{
Console.WriteLine("Ignoring extraneous scan.");
logfile.WriteLine("Ignoring extraneous scan.");
}
else
{
Console.Write('<');
planner_MUT.WaitOne();
Console.Write('_');
runProgram.receiveScan(scandata);
scandata.Dispose();
planner_MUT.ReleaseMutex();
Console.Write('>');
logfile.Flush();
}
}
catch (Exception err)
{
Console.WriteLine("Caught error in scanArrived_response! Cancelling voltage.");
change_voltage(0);
Console.WriteLine(err.ToString());
throw;
}
}
private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
// If examining code takes longer, in particular for some scans, it is wise
// to use a processing queue in order to get the system as responsive as possible.
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
Console.WriteLine("\n{0:HH:mm:ss,fff} scan with {1} centroids arrived", DateTime.Now, scan.CentroidCount);
#if ProfileAccessInsideEnumeration
int max = 5;
foreach (ICentroid c in scan.Centroids)
{
if (max-- == 0)
{
break;
}
Console.Write("{0:F4},{1:0.0e0},z={2} : ", c.Mz, c.Intensity, c.Charge);
// Access to profile information is done INSIDE the enumeration of centroids: profile is available:
Console.WriteLine(string.Join("; ", c.Profile.Take(5).Select(n => string.Format("{0:F4},{1:0.0e0}", n.Mz, n.Intensity))));
}
#elif ProfileAccessOutsideEnumeration
ICentroid[] list = scan.Centroids.ToArray();
for (int i = 0; i < Math.Min(5, list.Length); i++)
{
ICentroid c = list[i];
Console.Write("{0:F4},{1:0.0e0},z={2} : ", c.Mz, c.Intensity, c.Charge); // works
// Access to profile information is done OUTSIDE the enumeration of centroids, which is done by ToArray(), no profile is available:
Console.WriteLine(string.Join("; ", c.Profile.Take(5).Select(n => string.Format("{0:F4},{1:0.0e0}", n.Mz, n.Intensity)))); // crashes
}
#else
// Create an array where the profile is copied on enumeration if the above solution with ProfileAccessInsideEnumeration
// does not fit. The way of processing shown here requies more memory and is slower.
Tuple <ICentroid, IMassIntensity[]>[] list = scan.Centroids.Select(n => new Tuple <ICentroid, IMassIntensity[]>(n, (IMassIntensity[])n.Profile.Clone())).ToArray();
for (int i = 0; i < Math.Min(5, list.Length); i++)
{
Tuple <ICentroid, IMassIntensity[]> tuple = list[i];
Console.Write("{0:F4},{1:0.0e0},z={2} : ", tuple.Item1.Mz, tuple.Item1.Intensity, tuple.Item1.Charge); // works
Console.WriteLine(string.Join("; ", tuple.Item2.Take(5).Select(n => string.Format("{0:F4},{1:0.0e0}", n.Mz, n.Intensity)))); // works
}
#endif
}
}
void _instMSScanContainer_MsScanArrived(object sender, MsScanEventArgs e)
{
var lastScan1 = _instMSScanContainer.GetLastMsScan();
var lastScan2 = e.GetScan();
if (lastScan1 == lastScan2)
{
totalScansArrived++;
}
string accessID = "n/a";
lastScan1.Trailer.TryGetValue("Access ID", out accessID);
Invoke(new Action(
() =>
{
textBox1.Text = totalScansArrived.ToString();
textBox3.Text = accessID;
}));
}
private static void FusionScanContainer_MsScanArrived(object sender, MsScanEventArgs e)
{
// Print out the scan number of the scan received to console
Console.WriteLine("[{0:HH:mm:ss.ffff}] Received MS Scan Number: {1}",
DateTime.Now, e.GetScan().Header["Scan"]);
}