public static void PlaceFullScan(IScans m_scans, Parameters parameters)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.FullScanSetting.MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.FullScanSetting.MzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = parameters.FullScanSetting.MzRangeLowBound.ToString();
scan.Values["IsolationRangeHigh"] = parameters.FullScanSetting.MzRangeHighBound.ToString();
scan.Values["MaxIT"] = parameters.FullScanSetting.MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.FullScanSetting.Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString();
scan.Values["Microscans"] = parameters.FullScanSetting.Microscans.ToString();
scan.Values["AGC_Target"] = parameters.FullScanSetting.AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectRanges"] = "[]";
scan.Values["MsxInjectTargets"] = "[]";
scan.Values["MsxInjectMaxITs"] = "[]";
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing Full MS1 scan", DateTime.Now);
m_scans.SetCustomScan(scan);
}
/// <summary>
/// Dump the list of possible commands.
/// </summary>
/// <param name="scans">where to take possible parameters from</param>
/// <param name="verbose">shall each parameter be dumped?</param>
static private bool DumpPossibleParameters(IScans scans, bool verbose)
{
IParameterDescription[] parameters = scans.PossibleParameters;
if (parameters.Length == 0)
{
Console.WriteLine("No possible IScans parameters known.");
return(false);
}
if (verbose)
{
Console.WriteLine("IScans parameters:");
foreach (IParameterDescription parameter in parameters)
{
StringBuilder sb = new StringBuilder();
sb.AppendFormat(" '{0}' ", parameter.Name);
if (parameter.Selection == "")
{
sb.AppendFormat("doesn't accept an argument, help: {0}", parameter.Help);
}
else
{
sb.AppendFormat("accepts '{0}', default='{1}', help: {2}", parameter.Selection, parameter.DefaultValue, parameter.Help);
}
Console.WriteLine(sb.ToString());
}
}
else
{
Console.WriteLine("IScans parameters: {0}", string.Join(", ", parameters.Select(n => n.Name).ToArray()));
}
return(true);
}
/// <summary>
/// Create a new <see cref="ScansTest"/> and start the performance test immediately.
/// </summary>
/// <param name="instrument">the instrument instance</param>
/// <param name="arguments">program arguments</param>
internal ScansTest(IExactiveInstrumentAccess instrument, Arguments arguments)
{
Arguments = arguments;
m_scans = instrument.Control.GetScans(false);
m_scans.CanAcceptNextCustomScan += new EventHandler(Scans_CanAcceptNextCustomScan);
m_scans.PossibleParametersChanged += new EventHandler(Scans_PossibleParametersChanged);
DumpPossibleParameters();
bool startNewScan = false;
lock (m_lock)
{
if (m_scans.PossibleParameters.Length > 0)
{
startNewScan = m_startCustomScan;
m_startCustomScan = false;
}
}
if (startNewScan)
{
StartNewScan();
}
}
/// <summary>
/// Gets a scan information
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='cancellationToken'>
/// The cancellation token.
/// </param>
public static async Task <Scan> GetAsync(this IScans operations, string dataSourceName, string scanName, CancellationToken cancellationToken = default(CancellationToken))
{
using (var _result = await operations.GetWithHttpMessagesAsync(dataSourceName, scanName, null, cancellationToken).ConfigureAwait(false))
{
return(_result.Body);
}
}
/// <summary>
/// List scans in data source
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='skipToken'>
/// </param>
/// <param name='cancellationToken'>
/// The cancellation token.
/// </param>
public static async Task <ScanList> ListByDataSourceAsync(this IScans operations, string dataSourceName, string skipToken = default(string), CancellationToken cancellationToken = default(CancellationToken))
{
using (var _result = await operations.ListByDataSourceWithHttpMessagesAsync(dataSourceName, skipToken, null, cancellationToken).ConfigureAwait(false))
{
return(_result.Body);
}
}
/// <summary>
/// Runs the scan
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='body'>
/// </param>
/// <param name='cancellationToken'>
/// The cancellation token.
/// </param>
public static async Task <OperationResponse> RunAsync(this IScans operations, string dataSourceName, string scanName, ScanRunProperties body = default(ScanRunProperties), CancellationToken cancellationToken = default(CancellationToken))
{
using (var _result = await operations.RunWithHttpMessagesAsync(dataSourceName, scanName, body, null, cancellationToken).ConfigureAwait(false))
{
return(_result.Body);
}
}
public static void PlaceDynamicBoxCarScan_BU(IScans m_scans, Parameters parameters, List <List <Tuple <double, double, double> > > dynamicBoxs)
{
foreach (var dynamicBox in dynamicBoxs)
{
if (dynamicBox.Count > 0)
{
PlaceDynamicBoxCarScan(m_scans, parameters, dynamicBox.ToArray());
}
}
}
public override void Initialize(IScans machine_scan_manager)
{
ScanManager = machine_scan_manager;
scan_queue = new ConcurrentQueue <ICustomScan>();
MS1_outstanding = false;
RunTimer = new Stopwatch();
RunTimer.Start();
//exclusion_time_interval = TimeSpan.FromSeconds(10);
MS1_tardiness = new Stopwatch();
MS1_expiration_span = TimeSpan.FromSeconds(10);
}
public override void Initialize(IScans machine_scan_manager)
{
ScanManager = machine_scan_manager;
scan_queue = new ConcurrentQueue <ICustomScan>();
RunTimer = new Stopwatch();
RunTimer.Start();
mz_exclusion_intervals = new Dictionary <double, TimeSpan>();
MS1_tardiness = new Stopwatch();
MS1_expiration_span = TimeSpan.FromSeconds(3);
}
internal void DoJob()
{
using (IExactiveInstrumentAccess instrument = Connection.GetFirstInstrument())
{
using (m_scans = instrument.Control.GetScans(false))
{
IMsScanContainer orbitrap = instrument.GetMsScanContainer(0);
Console.WriteLine("Waiting 60 seconds for scans on detector " + orbitrap.DetectorClass + "...");
orbitrap.MsScanArrived += Orbitrap_MsScanArrived;
Thread.CurrentThread.Join(60000);
orbitrap.MsScanArrived -= Orbitrap_MsScanArrived;
}
}
}
/// <summary>
/// Cancel an outstanding repetition scan.
/// </summary>
/// <param name="access">used to get access to the needed IScans interface.</param>
static internal void CancelRepeatingScan(IExactiveInstrumentAccess access)
{
try
{
using (IScans scans = access.Control.GetScans(false))
{
if (!scans.CancelRepetition())
{
Console.WriteLine("CANCELLATION OF THE REPETITION SCAN HAS NOT BEEN PERFORMED, CONNECTION TO SERVICE BROKEN.");
}
}
}
catch (Exception e)
{
Console.WriteLine("CANCELING A REPETITION SCAN: " + e.Message);
}
}
public static void PlaceMS2Scan(IScans m_scans, Parameters parameters, List <double> dynamicBox)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
double Range = parameters.MS1IonSelecting.IsolationWindow;
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.MS2ScanSetting.MS2MzRangeHighBound.ToString(); //TO THINK: Dynamic range as MqLive?
scan.Values["IsolationRangeLow"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["IsolationRangeHigh"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["MaxIT"] = parameters.MS2ScanSetting.MS2MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = parameters.MS2ScanSetting.NCE.ToString();
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
if (parameters.MS2ScanSetting.NCE_factors != "null")
{
scan.Values["NCE_Factors"] = parameters.MS2ScanSetting.NCE_factors;
}
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.MS2ScanSetting.MS2MicroScans.ToString();
scan.Values["AGC_Target"] = parameters.MS2ScanSetting.MS2AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
string dynamicTargets;
string dynamicMaxIts;
var dynamicBoxString = BuildDynamicBoxInclusionString(parameters, dynamicBox, out dynamicTargets, out dynamicMaxIts);
scan.Values["MsxInjectRanges"] = dynamicBoxString;
scan.Values["MsxInjectTargets"] = dynamicTargets;
scan.Values["MsxInjectMaxITs"] = dynamicMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing data dependent ms2 scan {1}", DateTime.Now, dynamicBoxString);
m_scans.SetCustomScan(scan);
}
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;
}
}
}
/// <summary>
/// Set a default repeating scan with a FirstMass of 400.
/// </summary>
/// <param name="access">used to get access to the needed IScans interface.</param>
/// <param name="verbose">shall the output be verbose?</param>
static internal bool SetRepeatingScan(IExactiveInstrumentAccess access, bool verbose)
{
try
{
using (IScans scans = access.Control.GetScans(false))
{
bool parametersArrived = (scans.PossibleParameters.Length != 0);
// Test if we have to wait for arrival of possible parameters:
if (!parametersArrived)
{
EventHandler handler = (sender, args) => { parametersArrived = true; };
scans.PossibleParametersChanged += handler;
DateTime end = DateTime.Now.AddSeconds(3);
// Not elegant, but it works
while (!parametersArrived && (DateTime.Now < end))
{
// Sleep but perform COM communication in background.
Thread.CurrentThread.Join(10);
}
scans.PossibleParametersChanged -= handler;
// Fall into an error below if we didn't receive parameter descriptions.
}
DumpPossibleParameters(scans, verbose);
IRepeatingScan scan = scans.CreateRepeatingScan();
scan.RunningNumber = 9999;
scan.Values["FirstMass"] = "400";
if (scans.SetRepetitionScan(scan))
{
return(true);
}
Console.WriteLine("SETTING A REPETITION SCAN HAS NOT BEEN DONE, CONNECTION TO SERVICE BROKEN.");
}
}
catch (Exception e)
{
Console.WriteLine("SETTING A REPETITION SCAN: " + e.Message);
}
return(false);
}
//parameter Tuple<double, double, double> for each box start m/z, end m/z, m/z length
public static void PlaceDynamicBoxCarScan(IScans m_scans, Parameters parameters, Tuple <double, double, double>[] dynamicBox)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = (parameters.BoxCarScanSetting.BoxCarMzRangeLowBound - 200).ToString();
scan.Values["IsolationRangeHigh"] = (parameters.BoxCarScanSetting.BoxCarMzRangeHighBound + 200).ToString();
scan.Values["MaxIT"] = parameters.BoxCarScanSetting.BoxCarMaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.BoxCarScanSetting.BoxCarResolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.BoxCarScanSetting.BoxCarNormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.BoxCarScanSetting.BoxCarMicroScans.ToString();
scan.Values["AGC_Target"] = parameters.BoxCarScanSetting.BoxCarAgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
string dynamicTargets;
string dynamicMaxIts;
var dynamicBoxString = BuildDynamicBoxString(parameters, dynamicBox, out dynamicTargets, out dynamicMaxIts);
scan.Values["MsxInjectRanges"] = dynamicBoxString;
scan.Values["MsxInjectTargets"] = dynamicTargets;
scan.Values["MsxInjectMaxITs"] = dynamicMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
Console.WriteLine("{0:HH:mm:ss,fff} placing Dynamic BoxCar MS1 scan {1}", DateTime.Now, dynamicBoxString);
m_scans.SetCustomScan(scan);
}
/// <summary>
/// Clean up any resources being used.
/// </summary>
/// <param name="disposeEvenManagedStuff">true to dispose managed and unmanaged resources; false to dispose unmanaged resources</param>
protected void Dispose(bool disposeEvenManagedStuff)
{
// prevent double disposing
if (Interlocked.Exchange(ref m_disposed, 1) != 0)
{
return;
}
if (disposeEvenManagedStuff)
{
if (m_scans != null)
{
m_scans.CanAcceptNextCustomScan -= new EventHandler(Scans_CanAcceptNextCustomScan);
m_scans.PossibleParametersChanged -= new EventHandler(Scans_PossibleParametersChanged);
m_scans.Dispose();
m_scans = null;
}
}
}
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;
}
}
}
/// <summary>
/// Wait up to 10 seconds to see the list of parameters for scans. Before that we cannot place scans.
/// </summary>
/// <param name="scans">interface to use</param>
private void WaitFor(IScans scans)
{
Console.WriteLine("{0:HH:mm:ss,fff} waiting for IScans interface to become ready", DateTime.Now);
ManualResetEvent wait = new ManualResetEvent(false);
EventHandler handler = (sender, e) => { wait.Set(); };
scans.PossibleParametersChanged += handler;
if ((scans.PossibleParameters != null) && (scans.PossibleParameters.Length > 0))
{
wait.Set();
}
wait.WaitOne(10000);
scans.PossibleParametersChanged -= handler;
if ((scans.PossibleParameters == null) || (scans.PossibleParameters.Length == 0))
{
throw new TimeoutException("Not connected to the instrument or something else happened.");
}
Console.WriteLine("{0:HH:mm:ss,fff} end of wait", DateTime.Now);
}
public static void PlaceStaticBoxCarScan(IScans m_scans, Parameters parameters)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.BoxCarScanSetting.BoxCarMzRangeHighBound.ToString();
scan.Values["IsolationRangeLow"] = (parameters.BoxCarScanSetting.BoxCarMzRangeLowBound).ToString();
scan.Values["IsolationRangeHigh"] = (parameters.BoxCarScanSetting.BoxCarMzRangeHighBound).ToString();
scan.Values["MaxIT"] = parameters.BoxCarScanSetting.BoxCarMaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.BoxCarScanSetting.BoxCarResolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = "0.0";
scan.Values["NCE_NormCharge"] = parameters.BoxCarScanSetting.BoxCarNormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
scan.Values["NCE_Factors"] = "[]";
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.BoxCarScanSetting.BoxCarMicroScans.ToString();
scan.Values["AGC_Target"] = parameters.BoxCarScanSetting.BoxCarAgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectTargets"] = StaticBoxCarScanTargets;
scan.Values["MsxInjectMaxITs"] = StaticBoxCarScanMaxIts;
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
for (int i = 0; i < parameters.BoxCarScanSetting.NumberOfBoxCarScans; i++)
{
scan.Values["MsxInjectRanges"] = StaticBoxCarScanRanges[i];
Console.WriteLine("{0:HH:mm:ss,fff} placing BoxCar MS1 scan", DateTime.Now);
m_scans.SetCustomScan(scan);
}
}
/// <summary>
/// Runs the scan
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='body'>
/// </param>
public static OperationResponse Run(this IScans operations, string dataSourceName, string scanName, ScanRunProperties body = default(ScanRunProperties))
{
return(operations.RunAsync(dataSourceName, scanName, body).GetAwaiter().GetResult());
}
public static void PlaceMS2Scan(IScans m_scans, Parameters parameters, double mz)
{
if (m_scans.PossibleParameters.Length == 0)
{
return;
}
double Range = parameters.MS1IonSelecting.IsolationWindow;
string xl = (mz - Range).ToString("0.000");
string xh = (mz + Range).ToString("0.000");
if (mz - Range < 50.0)
{
Console.WriteLine("placing data dependent ms2 scan wrong, the Ms2MzRangeLowBound should larger than 50!!!");
return;
}
ICustomScan scan = m_scans.CreateCustomScan();
scan.Values["FirstMass"] = parameters.MS2ScanSetting.MS2MzRangeLowBound.ToString();
scan.Values["LastMass"] = parameters.MS2ScanSetting.MS2MzRangeHighBound.ToString(); //TO THINK: Dynamic range as MqLive?
scan.Values["IsolationRangeLow"] = xl;
scan.Values["IsolationRangeHigh"] = xh;
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["MaxIT"] = parameters.MS2ScanSetting.MS2MaxInjectTimeInMillisecond.ToString();
scan.Values["Resolution"] = parameters.MS2ScanSetting.MS2Resolution.ToString();
scan.Values["Polarity"] = parameters.GeneralSetting.Polarity.ToString();
scan.Values["NCE"] = parameters.MS2ScanSetting.NCE.ToString();
scan.Values["NCE_NormCharge"] = parameters.MS1IonSelecting.NormCharge.ToString();
scan.Values["NCE_SteppedEnergy"] = "0";
if (parameters.MS2ScanSetting.NCE_factors != "null")
{
scan.Values["NCE_Factors"] = parameters.MS2ScanSetting.NCE_factors;
}
scan.Values["SourceCID"] = parameters.GeneralSetting.SourceCID.ToString("0.00");
scan.Values["Microscans"] = parameters.MS2ScanSetting.MS2MicroScans.ToString();
scan.Values["AGC_Target"] = parameters.MS2ScanSetting.MS2AgcTarget.ToString();
scan.Values["AGC_Mode"] = parameters.GeneralSetting.AGC_Mode.ToString();
scan.Values["MsxInjectRanges"] = "[]";
scan.Values["MsxInjectTargets"] = "[]";
scan.Values["MsxInjectMaxITs"] = "[]";
scan.Values["MsxInjectNCEs"] = "[]";
scan.Values["MsxInjectDirectCEs"] = "[]";
//Console.WriteLine("++++++++++++++++++");
//Console.WriteLine("Target Isolation Mass: {0}, {1}", xl, xh);
//foreach (var v in scan.Values)
//{
// Console.WriteLine(v);
//}
////This is the code where we find all the scan settings.
////foreach (var item in m_scans.PossibleParameters)
////{
//// Console.WriteLine(item.Name + "----" + item.DefaultValue + "----" + item.Help + "----" + item.Selection);
////}
Console.WriteLine("{0:HH:mm:ss,fff} placing data dependent ms2 scan {1}", DateTime.Now, mz);
m_scans.SetCustomScan(scan);
}
/// <summary>
/// List scans in data source
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='skipToken'>
/// </param>
public static ScanList ListByDataSource(this IScans operations, string dataSourceName, string skipToken = default(string))
{
return(operations.ListByDataSourceAsync(dataSourceName, skipToken).GetAwaiter().GetResult());
}
/// <summary>
/// Deletes the scan associated with the data source
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
public static void Delete(this IScans operations, string dataSourceName, string scanName)
{
operations.DeleteAsync(dataSourceName, scanName).GetAwaiter().GetResult();
}
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);
}
/// <summary>
/// Creates an instance of a scan
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='body'>
/// </param>
public static Scan CreateOrUpdate(this IScans operations, string dataSourceName, string scanName, Scan body)
{
return(operations.CreateOrUpdateAsync(dataSourceName, scanName, body).GetAwaiter().GetResult());
}
public abstract void Initialize(IScans machine_scan_manager);
private void button3_Click(object sender, EventArgs e)
{
_instAccess = _instAccessContainer.Get(1);
instrumentIdTB.Text = _instAccess.InstrumentId.ToString();
instrumentNameTB.Text = _instAccess.InstrumentName;
instrumentConnectedTB.Text = _instAccess.Connected.ToString();
_instControl = _instAccess.Control;
_instAccess.ConnectionChanged += _instAccess_ConnectionChanged;
_instAccess.ContactClosureChanged += _instAccess_ContactClosureChanged;
_instAcq = _instControl.Acquisition;
_instAcq.StateChanged += Acquisition_StateChanged;
_instAcq.AcquisitionStreamClosing += _instAcq_AcquisitionStreamClosing;
_instAcq.AcquisitionStreamOpening += _instAcq_AcquisitionStreamOpening;
UpdateState(_instAcq.State);
_instValues = _instControl.InstrumentValues;
_scans = _instControl.GetScans(false);
_scans.CanAcceptNextCustomScan += _scans_CanAcceptNextCustomScan;
_scans.PossibleParametersChanged += _scans_PossibleParametersChanged;
scanProperties = new DataTable();
var propColumn = scanProperties.Columns.Add("Property", typeof(string));
propColumn.ReadOnly = true;
scanProperties.Columns.Add("Value", typeof(string));
scanProperties.Columns.Add("Selection", typeof(string)).ReadOnly = true;
scanProperties.Columns.Add("Help", typeof(string)).ReadOnly = true;
BindingSource source = new BindingSource();
source.DataSource = scanProperties;
dataGridView1.DataSource = source;
UpdateScanProperties();
_syringe = _instControl.SyringePumpControl;
_syringe.ParameterValueChanged += _syringe_ParameterValueChanged;
_syringe.StatusChanged += _syringe_StatusChanged;
updateSyringeReadbacks(true);
_instMSScanContainer = _instAccess.GetMsScanContainer(0);
// Analog Values
int numOfAnalogs = _instAccess.CountAnalogChannels;
_analogTrace = new IAnalogTraceContainer[numOfAnalogs];
for (int i = 0; i < numOfAnalogs; i++)
{
var trace = _analogTrace[i] = _instAccess.GetAnalogTraceContainer(i);
if (trace != null)
{
analogGroupBoxes[i].Text = trace.DetectorClass;
}
}
}
/// <summary>
/// Cancels a scan
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='body'>
/// </param>
public static void Cancel(this IScans operations, string dataSourceName, string scanName, CancelScanRequest body)
{
operations.CancelAsync(dataSourceName, scanName, body).GetAwaiter().GetResult();
}
/// <summary>
/// Cancels a scan
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
/// <param name='body'>
/// </param>
/// <param name='cancellationToken'>
/// The cancellation token.
/// </param>
public static async Task CancelAsync(this IScans operations, string dataSourceName, string scanName, CancelScanRequest body, CancellationToken cancellationToken = default(CancellationToken))
{
(await operations.CancelWithHttpMessagesAsync(dataSourceName, scanName, body, null, cancellationToken).ConfigureAwait(false)).Dispose();
}
/// <summary>
/// Gets a scan information
/// </summary>
/// <param name='operations'>
/// The operations group for this extension method.
/// </param>
/// <param name='dataSourceName'>
/// </param>
/// <param name='scanName'>
/// </param>
public static Scan Get(this IScans operations, string dataSourceName, string scanName)
{
return(operations.GetAsync(dataSourceName, scanName).GetAwaiter().GetResult());
}