internal void DoJob(ExclusionProfile exclusionProfile)
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
if (instrument == null)
{
Console.WriteLine("Failed to create Instrument, program will now exit");
return;
}
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
//if (GlobalVar.SeeExclusionFormat)
//{
// m_methods = instrument.Control.Methods;
// m_replacementTable = CreateReplacementTable();
//}
Console.WriteLine("Waiting 60 seconds for scans on detector " + orbitrap.DetectorClass + "...");
DataProcessor.reset();
Thread DataProcessingThread = new Thread(() => DataProcessor.StartProcessing(exclusionProfile));
//Thread InputHandling = new Thread(() => InputHandler.ReadConsoleInput());
DataProcessingThread.Start();
//InputHandling.Start();
while (!DataProcessor.SetupFinished())
{
Thread.Sleep(500);
}
orbitrap.AcquisitionStreamOpening += Orbitrap_AcquisitionStreamOpening;
orbitrap.AcquisitionStreamClosing += Orbitrap_AcquisitionStreamClosing;
Console.WriteLine("Waiting on acquisition stream to open");
while (!acquisitionStreamOpened && !Console.ReadKey().KeyChar.ToString().Equals("y"))
{
Console.WriteLine("Waiting on acquisition stream to open");
Thread.CurrentThread.Join(1000);
}
Console.WriteLine("MSScan Arrive event listener added");
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
int durationCounter = 0;
while (durationCounter < GlobalVar.listeningDuration && (ExclusionExplorer.IsListening()))
{
Thread.CurrentThread.Join(1000); //does the same thing as Thread.Sleep() but Join
//allows standard sendmessage pumping and COM to continue
durationCounter++;
}
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
orbitrap.AcquisitionStreamClosing -= Orbitrap_AcquisitionStreamClosing;
orbitrap.AcquisitionStreamOpening -= Orbitrap_AcquisitionStreamOpening;
DataProcessor.EndProcessing();
DataProcessingThread.Join(); //wait until dataProcessor finishes processing/outputing the scan
//queue then returns to Main thread;
}
}
internal void DoJob()
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
Console.WriteLine("Waiting 60 seconds for scans on detector " + orbitrap.DetectorClass + ", showing centroids...");
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
Thread.CurrentThread.Join(60000);
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
}
}
/// <summary>
/// Crate a new <see cref="ScansOutput"/>
/// </summary>
/// <param name="instrument">the instrument instance</param>
/// <param name="arguments">program arguments</param>
internal ScansOutput(IExactiveInstrumentAccess instrument, Arguments arguments)
{
Arguments = arguments;
ScanContainer = instrument.GetMsScanContainer(0);
if (Arguments.Verbose)
{
Console.WriteLine("Detector class: " + ScanContainer.DetectorClass);
}
ScanContainer.AcquisitionStreamOpening += new EventHandler <MsAcquisitionOpeningEventArgs>(ScanContainer_AcquisitionStarted);
ScanContainer.AcquisitionStreamClosing += new EventHandler(ScanContainer_AcquisitionEnded);
ScanContainer.MsScanArrived += new EventHandler <MsScanEventArgs>(ScanContainer_ScanArrived);
}
internal void DoJob()
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
m_methods = instrument.Control.Methods;
// don't know the time for powering up the table ==> do it (once) in advance of its use
m_replacementTable = CreateReplacementTable();
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
Console.WriteLine("Waiting 60 seconds for a starting acquisition...");
orbitrap.AcquisitionStreamOpening += Orbitrap_AcquisitionStreamOpening;
Thread.CurrentThread.Join(60000);
orbitrap.AcquisitionStreamOpening -= Orbitrap_AcquisitionStreamOpening;
}
}
internal void DoJob(int time)
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
using (m_scans = instrument.Control.GetScans(false))
{
m_scans.CanAcceptNextCustomScan += Scans_CanAcceptNextCustomScan;
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
Console.WriteLine("Waiting for scans on detector " + orbitrap.DetectorClass + "...");
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
Thread.CurrentThread.Join(time);
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
m_scans.CanAcceptNextCustomScan -= Scans_CanAcceptNextCustomScan;
}
}
}
internal void DoJob()
{
Thread childThreadCheckTime = new Thread(CheckTime);
childThreadCheckTime.IsBackground = true;
childThreadCheckTime.Start();
Console.WriteLine("Start Thread for checking time!");
if (Parameters.GeneralSetting.MethodType == MethodTypes.DynamicBoxCar_TD)
{
Thread childThreadDBCExclusionList = new Thread(DynamicDBCExclusionListDeque);
childThreadDBCExclusionList.IsBackground = true;
childThreadDBCExclusionList.Start();
Console.WriteLine("Start Thread for DynamicBoxCar (DBC) exclusion list!");
}
Thread childThreadExclusionList = new Thread(DynamicExclusionListDeqeue);
childThreadExclusionList.IsBackground = true;
childThreadExclusionList.Start();
Console.WriteLine("Start Thread for exclusion list!");
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
using (m_scans = instrument.Control.GetScans(false))
{
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
Console.WriteLine("Waiting for scans on detector " + orbitrap.DetectorClass + "...");
orbitrap.AcquisitionStreamOpening += Orbitrap_AcquisitionStreamOpening;
orbitrap.AcquisitionStreamClosing += Orbitrap_AcquisitionStreamClosing;
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
Thread.CurrentThread.Join(Parameters.GeneralSetting.TotalTimeInMinute * 60000);
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
orbitrap.AcquisitionStreamClosing -= Orbitrap_AcquisitionStreamClosing;
orbitrap.AcquisitionStreamOpening -= Orbitrap_AcquisitionStreamOpening;
}
}
}
public void RunMachine(Planner runManager, string filename, bool auto)
{
runProgram = runManager;
// Instrument access setup stuff.
if (!auto)
{
Console.WriteLine("Ready. (Press any key.)");
Console.ReadKey();
}
string device_registration = ((IntPtr.Size > 4) ? @"SOFTWARE\Wow6432Node\Finnigan\Xcalibur\Devices\" : @"SOFTWARE\Finnigan\Xcalibur\Devices\") + "Thermo Exactive";
string asmName = "None";
string typeName = "None";
RegistryKey key = Registry.LocalMachine.OpenSubKey(device_registration);
Debug.Assert(key != null);
asmName = (string)key.GetValue("ApiFileName_Clr2_32_V1", null);
typeName = (string)key.GetValue("ApiClassName_Clr2_32_V1", null);
Console.WriteLine("ASM: " + asmName + "\nType: " + typeName);
Directory.SetCurrentDirectory(Path.GetDirectoryName(asmName));
Assembly asm = Assembly.LoadFrom(asmName);
object api_obj = asm.CreateInstance(typeName);
container = api_obj as IInstrumentAccessContainer;
Debug.Assert(container != null);
instrument = container.Get(1);
Debug.Assert(instrument != null);
iexactive = instrument as IExactiveInstrumentAccess;
Debug.Assert(iexactive != null);
control = iexactive.Control;
acquisition = control.Acquisition as IExactiveAcquisition;
scanner = control.GetScans(false);
runProgram.Initialize(scanner);
// Attaching a simple function to on-new-scan event; equivalent of wx.Bind.
IMsScanContainer scancontainer = iexactive.GetMsScanContainer(0);
scancontainer.AcquisitionStreamOpening += new EventHandler <MsAcquisitionOpeningEventArgs>(goahead_Response);
scancontainer.AcquisitionStreamClosing += new EventHandler(stop_Response);
scancontainer.MsScanArrived += new EventHandler <MsScanEventArgs>(scanArrived_Response);
scanner.CanAcceptNextCustomScan += new EventHandler(readyForScan_Response);
acquisition.StateChanged += new EventHandler <StateChangedEventArgs>(note_state_change);
machine_voltage = control.InstrumentValues.Get("SourceSprayVoltage");
machine_voltage.ContentChanged += new EventHandler <Thermo.Interfaces.InstrumentAccess_V1.Control.ContentChangedEventArgs>(voltageChangeResponse);
Thread.Sleep(100); // Gives machine_voltage a chance to get its act together.
current_voltage = Double.Parse(machine_voltage.Content.Content);
change_voltage(0);
// Submitting method and running.
Console.WriteLine("Starting State=" + acquisition.State.SystemState);
// Attempts to control machine state; should be "On" after this code block.
ChangeResult set_to_standby_result = acquisition.SetMode(acquisition.CreateForcedStandbyMode());
acquisition.WaitFor(TimeSpan.FromSeconds(3), SystemMode.Standby);
ChangeResult set_to_on_result = acquisition.SetMode(acquisition.CreateOnMode());
acquisition.WaitFor(TimeSpan.FromSeconds(3), SystemMode.On);
authorized_for_run = false;
accepting_scans = false;
IAcquisitionWorkflow methodWorkflow = null;
methodWorkflow = acquisition.CreatePermanentAcquisition();
methodWorkflow.RawFileName = filename; // Numbers are appended to file name on overwrite.
if (USE_CONTACT_CLOSURE)
{
ITrigger ccTrigger = acquisition.CreateTrigger("WaitForContactClosure");
methodWorkflow.Trigger = ccTrigger;
}
else
{
authorized_for_run = true;
Console.WriteLine("NON-CONTACT CLOSURE START.");
}
ChangeResult start_acq_result = acquisition.StartAcquisition(methodWorkflow);
//methodWorkflow.SingleProcessingDelay = 600.0D; // Doesn't work!
run_is_active = true;
intendedRunTime = TimeSpan.FromSeconds(intended_run_seconds);
runTimeKeeper = new Stopwatch();
Console.WriteLine("Waiting for goahead...");
while (!authorized_for_run)
{
Thread.Sleep(100);
}
Console.WriteLine("Got goahead.");
Thread.Sleep(column_wait_time_seconds * 1000);
Console.WriteLine("Column wait over, setting charge up.");
change_voltage(working_voltage);
bool got_to_workable_state = acquisition.WaitFor(TimeSpan.FromSeconds(5), SystemMode.On, SystemMode.DirectControl);
if (!got_to_workable_state)
{
Console.WriteLine("Invalid state " + acquisition.State.SystemMode + " before scan submission. Done.");
if (!auto)
{
Console.ReadKey();
}
Environment.Exit(0);
}
Console.WriteLine("Starting.");
runTimeKeeper.Start(); // This had been before contact closure confirmation!
accepting_scans = true;
Thread scan_handler = new Thread(scan_assignment_handler);
scan_handler.Start();
//Debug.Assert(!acquisition.WaitFor(intendedRunTime, SystemMode.Standby)); // Wait while things run; state shouldn't change.
// COULD PROBABLY do something with AcquisitionStreamClosing instead.
Console.WriteLine("In run loop.");
while (runTimeKeeper.Elapsed < intendedRunTime)
{
Thread.Sleep(100);
}
Console.WriteLine("Closing up.");
authorized_for_run = false;
accepting_scans = false;
//run_is_active = false;
//scan_handler.Abort();
scan_handler.Join();
Console.WriteLine("Joined.");
change_voltage(0);
ChangeResult cancel_result = acquisition.CancelAcquisition();
Console.WriteLine("Cancellation result: " + cancel_result.ToString());
Console.WriteLine("Setting mode to standby.");
ChangeResult setmode2_result = acquisition.SetMode(acquisition.CreateForcedStandbyMode());
Console.WriteLine("Set mode result: " + setmode2_result.ToString());
//if (run_is_active)
//{
// Console.WriteLine("Acquisition closed immediately/already.");
//} else
//{
// Console.WriteLine("Waiting for acquisition close event.");
// Stopwatch CloseTimer = new Stopwatch();
// CloseTimer.Start();
// while (run_is_active)
// {
// Thread.Sleep(100);
// }
// Console.WriteLine("Close event received after " + CloseTimer.Elapsed.ToString() + " seconds.");
//}
runManager.Cleanup();
Console.WriteLine("Safety wait.");
Thread.Sleep(15 * 1000); // Should match SingleProcessingDelay used by Planner.
Console.WriteLine("Done.");
if (!auto)
{
Console.ReadKey();
}
Environment.Exit(0);
}